Protein-protein interactions in neurodegenerative diseases

ABSTRACT

The present invention relates to the discovery of protein-protein interactions that are involved in the pathogenesis of neurodegenerative disorders, including Alzheimer&#39;s disease (AD). Thus, the present invention is directed to complexes of these proteins and/or their fragments, antibodies to the complexes, diagnosis of neurodegenerative disorders (including diagnosis of a predisposition to and diagnosis of the existence of the disorder), drug screening for agents which modulate the interaction of proteins described herein, and identification of additional proteins in the pathway common to the proteins described herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] The present application is related to U.S. provisional patentapplications Serial No. 60/240,790, filed on Oct. 17, 2000 and Ser. No.60/304,775 filed on Jul. 13, 2001, each incorporated herein byreference, and claims priority thereto under 35 USC §119(e).

BACKGROUND OF THE INVENTION

[0002] The present invention relates to the discovery of protein-proteininteractions that are involved in the pathogenesis of neurodegenerativedisorders, including Huntington's Disease, Parkinson's Disease, dementiaand Alzheimer's Disease (AD). Thus, the present invention is directed tocomplexes of these proteins and/or their fragments, antibodies to thecomplexes, diagnosis of neurodegenerative disorders (including diagnosisof a predisposition to and diagnosis of the existence of the disorder),drug screening for agents which modulate the interaction of proteinsdescribed herein, and identification of additional proteins in thepathway common to the proteins described herein.

[0003] The publications and other materials used herein to illuminatethe background of the invention, and in particular, cases to provideadditional details respecting the practice, are incorporated herein byreference, and for convenience, are referenced by author and date in thefollowing text and respectively grouped in the appended Bibliography.

[0004] Alzheimer's Disease (AD) is a neurodegenerative diseasecharacterized by a progressive decline of cognitive functions, includingloss or declarative and procedural memory, decreased learning ability,reduced attention span, and severe impairment in thinking ability,judgment, and decision making. Mood disorders and depression are alsooften observed in AD patients. It is estimated that AD affects about 4million people in the USA and 20 million people world wide. Because ADis an age-related disorder (with an average onset at 65 years), theincidence of the disease in industrialized countries is expected to risedramatically as the population of these countries is aging.

[0005] AD is characterized by the following neuropathological features:

[0006] a massive loss of neurons and synapses in the brain regionsinvolved in higher cognitive functions (association cortex, hippocampus,amygdala). Cholinergic neurons are particularly affected.

[0007] neuritic (senile) plaques that are composed of a core of amyloidmaterial surrounded by a halo of dystrophic neurites, reactive type Iastrocytes, and numerous microglial cells (Selkoe, 1994a; Selkoe, 1994c;Dickson, 1997; Hardy and Gwinn-Hardy, 1998; Selkoe, 1996b). The majorcomponent of the core is a peptide of 39 to 42 amino acids called theamyloid p protein, or Aβ. Although the Aβ protein is produced by theintracellular processing of its precursor, APP, the amyloid depositsforming the core of the plaques are extracellular. Studies have shownthat the longer form of Aβ (Aβ42) is much more amyloidogenic than theshorter forms (Aβ4O or Aβ39).

[0008] neurofibrillary tangles that are composed of paired-helicalfilaments (PHF) (Ray et al., 1998; Brion, 1998). Biochemical analysesrevealed that the main component of PHE is a hyper-phosphorylated formof the microtubule-associated protein T. These tangles are intracellularstructures, found in the cell body of dying neurons, as well as somedystrophic neurites in the halo surrounding neuritic plaques.

[0009] Both plaques and tangles are found in the same brain regionsaffected by neuronal and synaptic loss.

[0010] Although the neuronal and synaptic loss is universally recognizedas the primary cause of the decline of cognitive functions, thecellular, biochemical, and molecular events responsible for thisneuronal and synaptic loss are subject to fierce controversy. The numberof tangles shows a better correlation than the amyloid load with thecognitive decline (Albert, 1996). On the other hand, a number of studiesshowed that amyloid can be directly toxic to neurons (Iversen et al.,1995; Weiss et al., 1994; Lorenzo and Yankner, 1996; Storey and Cappai,1999), resulting in behavioral impairment (Ma et al., 1996). It has alsobeen shown that the toxicity of some compounds (amyloid or tangles)could be aggravated by activation of the complement cascade (Rogers etal., 1992b; Rozemuller et al., 1992; Rogers et al., 1992a; Webster etal., 1997), suggesting the possible involvement of inflammatory processin the neuronal death (Fagarasan and Aisen, 1996; Kalaria et al., 1996b;Kalaria et al., 1996a; Farlow, 1998).

[0011] Genetic and molecular studies of some familial forms of AD (FAD)have recently provided evidence that boosted the amyloid hypothesis (Ii,1995; Price et al., 1995; Hardy, 1997; Selkoe, 1996a). The assumption isthat since the deposition of Aβ in the core of senile plaques isobserved in all Alzheimer cases, if Aβ is the primary cause of AD, thenmutations that are linked to FAD should induce changes that, in a way oranother, foster Aβ deposition. There are 3 FAD genes known so far (Hardyand Gwinn-Hardy, 1998; Ray et al., 1998), and the activity of all ofthem results in increased Aβ deposition, a very compelling argument infavor of the amyloid hypothesis.

[0012] The first of the 3 FAD genes codes for the Aβ precursor, APP(Selkoe, 1996a). Mutations in the APP gene are very rare, but all ofthem cause AD with 100% penetrance and result in elevated production ofeither total Aβ or Aβ42, both in vitro (transfected cells) and in vivo(transgenic animals). The other two FAD genes code for presenilin 1 and2 (PS1, PS2) (Hardy, 1997). The presenilins contain 8 transmembranedomains and several lines of evidence suggest that they are involved inintracellular protein trafficking, although other studies suggest thatthey could function as proteases (see below). Mutations in thepresenilin genes are more common than in the APP genes, and all of themalso cause FAD with 100% penetrance. In addition, in vitro and in vivostudies have demonstrated that PS1 and PS2 mutations shift APPmetabolism, resulting in elevated Aβ42 production. For a recent reviewon the genetics of AD, see (Lippa, 1999).

[0013] In spite of these compelling genetic data, it is still unclearwhether Aβ generation and amyloid deposition are the primary cause ofneuronal death and synaptic loss observed in AD. Moreover, thebiochemical events leading to Aβ production, the relationship betweenAPP and the presenilins, and between amyloid and neurofibrillary tanglesare poorly understood. Thus, the picture of interactions between themajor Alzheimer proteins is very incomplete, and it is clear that alarge number of novel proteins are yet to be discovered. To this end, wehave initiated a systematic study looking at proteins interacting withvarious domains of the major Alzheimer proteins (see below). The resultsfrom these experiments provide a more complete understanding of theprotein-protein interactions involved in AD pathogenesis, and thus willgreatly help in the identification of a drug target. Because AD is aneurodegenerative disease, it is also expected that this project willidentify novel proteins involved in neuronal survival, neuriteoutgrowth, and maintenance of synaptic structures, thus openingopportunities into potentially any pathological condition in which theintegrity of neurons and synapses is threatened.

[0014] Thus, the picture of interactions between the major AD proteinsis very incomplete, and it is clear that a number of novel proteins areyet to be discovered. Although a number of molecules have beenidentified as possibly involved in the disease progression, noparticular protein (or set of proteins) has been identified as primarilyresponsible for the loss of neurons and synapses. More importantly, noneof the various components identified so far in the cascade of eventsleading to AD is a confirmed drug target.

[0015] There continues to be a need in the art for the discovery ofadditional proteins interacting with various domains of the majorAlzheimer proteins, including APP and the presenilins. There continuesto be a need in the art also to identify the protein-proteininteractions that are involved in AD pathogenesis, and to thus identifydrug targets.

SUMMARY OF THE INVENTION

[0016] The present invention relates to the discovery of protein-proteininteractions that are involved in the pathogenesis of neurodegenerativedisorders, including AD, and to the use of this discovery. Theidentification of the AD interacting proteins described herein providenew targets for the identification of useful pharmaceuticals, newtargets for diagnostic tools in the identification of individuals atrisk, sequences for production of transformed cell lines, cellularmodels and animal models, and new bases for therapeutic intervention inneurodegenerative disorders, including AD.

[0017] Thus, one aspect of the present invention are protein complexes.The protein complexes are a complex of (a) two interacting proteins, (b)a first interacting protein and a fragment of a second interactingprotein, (c) a fragment of a first interacting protein and a secondinteracting protein, or (d) a fragment of a first interacting proteinand a fragment of a second interacting protein. The fragments of theinteracting proteins include those parts of the proteins, which interactto form a complex. This aspect of the invention includes the detectionof protein interactions and the production of proteins by recombinanttechniques. The latter embodiment also includes cloned sequences,vectors, transfected or transformed host cells and transgenic animals.

[0018] A second aspect of the present invention is an antibody that isimmunoreactive with the above complex. The antibody may be a polyclonalantibody or a monoclonal antibody. While the antibody is immunoreactivewith the complex, it is not immunoreactive with the component parts ofthe complex. That is, the antibody is not immunoreactive with a firstinteractive protein, a fragment of a first interacting protein, a secondinteracting protein or a fragment of a second interacting protein. Suchantibodies can be used to detect the presence or absence of the proteincomplexes.

[0019] A third aspect of the present invention is a method fordiagnosing a predisposition for neurodegenerative disorders in a humanor other animal. The diagnosis of a neurodegenerative disorder includesa diagnosis of a predisposition to a neurodegenerative disorder and adiagnosis for the existence of a neurodegenerative disorder. In apreferred embodiment, the diagnosis is for AD. In accordance with thismethod, the ability of a first interacting protein or fragment thereofto form a complex with a second interacting protein or a fragmentthereof is assayed, or the genes encoding interacting proteins arescreened for mutations in interacting portions of the protein molecules.The inability of a first interacting protein or fragment thereof to forma complex, or the presence of mutations in a gene within the interactingdomain, is indicative of a predisposition to, or existence of aneurodegenerative disorder, such as AD. In accordance with oneembodiment of the invention, the ability to form a complex is assayed ina two-hybrid assay. In a first aspect of this embodiment, the ability toform a complex is assayed by a yeast two-hybrid assay. In a secondaspect, the ability to form a complex is assayed by a mammaliantwo-hybrid assay. In a second embodiment, the ability to form a complexis assayed by measuring in vitro a complex formed by combining saidfirst protein and said second protein. In one aspect the proteins areisolated from a human or other animal. In a third embodiment, theability to form a complex is assayed by measuring the binding of anantibody, which is specific for the complex. In a fourth embodiment, theability to form a complex is assayed by measuring the binding of anantibody that is specific for the complex with a tissue extract from ahuman or other animal. In a fifth embodiment, coding sequences of theinteracting proteins described herein are screened for mutations.

[0020] A fourth aspect of the present invention is a method forscreening for drug candidates which are capable of modulating theinteraction of a first interacting protein and a second interactingprotein. In this method, the amount of the complex formed in thepresence of a drug is compared with the amount of the complex formed inthe absence of the drug. If the amount of complex formed in the presenceof the drug is greater than or less than the amount of complex formed inthe absence of the drug, the drug is a candidate for modulating theinteraction of the first and second interacting proteins. The drugpromotes the interaction if the complex formed in the presence of thedrug is greater and inhibits (or disrupts) the interaction if thecomplex formed in the presence of the drug is less. The drug may affectthe interaction directly, i.e., by modulating the binding of the twoproteins, or indirectly, e.g., by modulating the expression of one orboth of the proteins.

[0021] A fifth aspect of the present invention is a model forneurodegenerative disorders, including AD. The model may be a cellularmodel or an animal model, as further described herein. In accordancewith one embodiment of the invention, an animal model is prepared bycreating transgenic or “knock-out” animals. The knock-out may be a totalknock-out, i.e., the desired gene is deleted, or a conditionalknock-out, i.e., the gene is active until it is knocked out at adetermined time. In a second embodiment, a cell line is derived fromsuch animals for use as a model. In a third embodiment, an animal modelis prepared in which the biological activity of a protein complex of thepresent invention has been altered. In one aspect, the biologicalactivity is altered by disrupting the formation of the protein complex,such as by the binding of an antibody or small molecule to one of theproteins which prevents the formation of the protein complex. In asecond aspect, the biological activity of a protein complex is alteredby disrupting the action of the complex, such as y the binding of anantibody or small molecule to the protein complex which interferes withthe action of the protein complex as described herein. In a fourthembodiment, a cell model is prepared by altering the genome of the cellsin a cell line. In one aspect, the genome of the cells is modified toproduce at least one protein complex described herein. In a secondaspect, the genome of the cells is modified to eliminate at least oneprotein of the protein complexes described herein.

[0022] A sixth aspect of the present invention are nucleic acids codingfor novel proteins discovered in accordance with the present invention.

[0023] A seventh aspect of the present invention is a method forscreening for drug candidates useful for treating a physiologicaldisorder. In this embodiment, drugs are screened on the basis of theassociation of a protein with a particular physiological disorder. Thisassociation is established in accordance with the present invention byidentifying a relationship of the protein with a particularphysiological disorder. The drugs are screened by comparing the activityof the protein in the presence and absence of the drug. If a differencein activity is found, then the drug is a drug candidate for thephysiological disorder. The activity of the protein can be assayed invitro or in vivo using conventional techniques, including transgenicanimals and cell lines of the present invention.

DETAILED DESCRIPTION OF THE INVENTION

[0024] The present invention is the discovery of novel interactionsbetween PS1, APP or other protein involved in AD and other proteins. Thegenes coding for these proteins have been cloned previously, but theirpotential involvement in AD was unknown. These proteins play a majorrole in AD and neurodegeneration, based in part on the discovery oftheir interactions and on their known biological functions. Theseproteins were identified using the yeast two-hybrid method and searchinga human total brain library, as more fully described below.

[0025] Although the senile plaque density and amyloid load do notcorrelate with cognitive decline, the genetic data strongly support acausal involvement of amyloid production in AD pathogenesis (Neve etal., 1990; Selkoe, 1994a; Octave, 1995; Roch et al., 1993; Saitoh, Roch,1995; Selkoe, 1994b; Selkoe, 1996a). The 3 genes identified so far thatcontain mutations known to cause AD are APP, PS1 and PS2. Because thenumber of AD mutations found in PS1 (over 50) is much larger than thenumber of AD mutations found in PS2 (only 2), most of the studieslooking at the involvement of the presenilins in AD have focused on PS1rather than PS2. As for APP, although the number of AD mutations in theAPP gene is small (5), the mere fact the APP is the biochemicalprecursor of Aβ put it in the heart of countless studies world wide.Thus, it is no surprise that the APP and PS1 gene products are alwaysfound as the major components of the description of events leading toneuronal death.

[0026] APP refers to a group of transmembrane proteins translated fromalternatively spliced mRNAs. The smallest isoform contains 695 aminoacids and is expressed almost exclusively in the brain, where it is themajor APP isoform. The other major isoforms, of 714, 751, and 770residues, contain either one or both domains of 19 and 51 residues withhomology to the OX-2 antigen and Kunitz type protease inhibitors,respectively. The metabolism of APP is complex, following severaldifferent pathways. APP can be secreted from cells such as PC12,fibroblasts, and neurons. The secretion event includes a cleavage stepof the precursor, releasing a large N-terminal portion of APP, sAPP,into the medium. The majority of cleavage is at the α-secretase site andoccurs within the Aβ domain between amino acids β16 and β17, andreleases sAPPα extracellularly. Thus, the processing of APP through theα-secretory pathway precludes the formation of intact Aβ protein. APPcan also follow a pathway that leads to the secretion of Aβ protein, aswell as sAPPβ, which is 15 amino acids shorter than sAPPα. Clearly, thispathway is potentially amyloidogenic. However, the secretion of Aβprotein is not the result of an aberrant processing of APP because itoccurs in cultured cells under normal physiological conditions, andsecreted Aβ protein has been detected in biological fluids from normalindividuals. The regulation of these two pathways involves bothPKC-dependent and PKC-independent phosphorylation reactions and is alsoaltered by some of the mutations within the APP molecule that cause ADin some Swedish families (see below).

[0027] Recently, the enzyme that cleaves APP at the β site (D597 ofAPP695) has been identified and its cDNA cloned (Vassar et al., 1999;Hussain et al., 1999). This β-secretase enzyme, called BACE or Asp-2, isa transmembrane protein of 501 residues which belongs to the AspartylProtease family. Although BACE is clearly able to cleave APP at the βsite, it is unclear whether APP is the natural physiological substrateof BACE. Cleavage of APP at the α site results in the secretion of sAPPαand recycling of an 83-residue non-amyloidogenic transmembraneC-terminal fragment, C83. Cleavage of APP at the β site results in thesecretion of sAPPβ and recycling of an 99-residue potentiallyamyloidogenic transmembrane C-terminal fragment, C99. After cleavage ofthe precursor at the α or β site, C83 and C99 can be further cleaved atthe so called γ site (APP636 to APP638), thus releasing the p3 fragmentor the Aβ peptide, respectively.

[0028] Recent studies suggest that PS1 and PS2 are capable of cleavingAPP at the γ site (Wolfe et al., 1999b; De Strooper et al., 1999; Wolfeet al., 1999a; Li et al.2000a; Li et al.2000b). However, it is stillunclear whether PS1 and PS2 are the only potential γ-secretases, or theyfunction as part of a large molecular complex or as purified proteins.It has recently been suggested that different γ-secretase activitiesoccur in different cellular compartments (Murphy et al., 1999), and thatPS1 might in fact regulate these pharmacologically distinct enzymaticactivities (Murphy et al.2000). The fact that the presenilins are oftenfound inside the cells as part of large molecular complex (Zhou et al.,1997b; Yu et al., 1998; Thinakaran et al., 1997; Yu et al.2000a)}suggests that other proteins are involved in the γ-secretase activity.Recently, a novel protein named nicastrin that binds both PS 1 and PS2as well as APP was shown to modulate the presenilin-mediated cleavage ofAPP at the γ site (Yu et al., 2000b). Thus, the exact function of thepresenilins in APP processing is not yet fully understood. The doublemutation located just upstream of the β-cleavage site (known as the“Swedish” mutation) was shown to shift the metabolism of APP from theα-secretase toward the β-secretase pathway, thus increasing theproduction of total Aβ. On the other hand, the Val717 mutations, locatedjust after the γ cleavage site do not alter the ratio of α vs βcleavage, but increase the ratio of Aβ42 vs total Aβ, thus making moreof the highly amyloidogenic form. Therefore, both types of mutationsalter the metabolism of APP in a way that results in elevated levels ofAβ42, thus fostering amyloid formation. For reviews on APP processingand its involvement in AD, see (Ashall and Goate, 1994; Selkoe, 1994a;Hardy, 1997; Selkoe, 1994b; Roch and Puttfarcken, 1996; Storey andCappai, 1999; Haass and De Strooper, 1999; Wolfe et al., 1999a; Selkoe,1999).

[0029] There is contradicting evidence as to the cellular location whereAPP is cleaved by the secretases (Price et al., 1995; Beyreuther et al.,1996; Leblanc et al., 1996; Caputi et al., 1997; Selkoe, 1997). Someinvestigators suggested that APP is cleaved in the trans-Golgi network(TGN) or in secretory vesicles en route to the plasma membrane, whileothers presented evidence that intact APP reaches the plasma membraneand is cleaved only after it is expressed at the cell surface. Differentcell types and expression systems could explain those discrepancies.However, it is now well established that either full-length APP or itsC-terminal fragment are recycled into the endosomal-lysosomalcompartment. The C-terminal fragments that contain the complete Aβdomain are transported further back to the TGN and endoplasmicreticulum, where Aβ40 and Aβ42 are produced, respectively. The free Aβfragments are then re-routed again toward the cell surface throughsecretory vesicles, and ultimately secreted into the extracellularmilieu, where the Aβ42 will seed the aggregation into amyloid material.Clearly, proteins that interact with the cytoplasmic tail of APP couldplay a major role in its intracellular traffic, thus its metabolism. Thecytoplasmic domain of APP was shown to interact with intracellularproteins Fe65, Fe65L, X11 , and X11L (McLoughlin and Miller, 1996;Blanco et al., 1998; Russo et al., 1998; Trommsdorffet al., 1998). Theseproteins have been localized in both the cytosol and the nucleus(Zambrano et al., 1998) and are thought to play a role in transcriptionregulation. In fact, Fe65 is known to interact with know transcriptionfactors Mena and LSF (Zambrano et al., 1998; Ermekova et al., 1997).There is also ample evidence that Fe65 and LSF influence theintracellular trafficking of APP, and thus indirectly control APPmetabolism (Russo et al., 1998; Sabo et al., 1999), a central event inAD pathogenesis.

[0030] The mechanism of Aβ toxicity is also highly controversial(Iversen et al., 1995; Manelli and Puttfarcken, 1995; Gillardon et al.,1996; Behl et al., 1992; Weiss et al., 1994; Octave, 1995; Furukawa etal., 1996b; Schubert, 1997). Some studies indicate that Aβ must be inthe aggregated amyloid form to be toxic. Other investigators showed thatsoluble Aβ is toxic and suggested that aggregation of soluble Aβ intoamyloid fibrils is a defense mechanism aiming at sequestering solubleAβ. While most studies found that Aβ is toxic to cells from the outside,a few investigators also found that Aβ can kill cells from the inside,before it is secreted. Whatever the exact mechanism is, a consensus isnow emerging, indicating that Aβ disrupts calcium homeostasis andtriggers the generation of free radicals and lipid peroxidation (Weisset al., 1994; Abe and Kimura, 1996; Mark et al., 1997; Kruman et al.,1997). Consistent with this idea, antioxidants (such as vitamin E) andneurotrophic factors that attenuate calcium influx (such as sAPP)protect neurons from Aβ mediated toxicity (Behl et al., 1992; Weiss etal., 1994).

[0031] After cleavage by the α-orβ-secretase,the N-terminal portion ofAPP is secreted into the extracellular milieu where it shows a widevariety of functions. The most relevant to AD are the neurotrophic andneuroprotective activities. A number of in vitro studies have shown thatsAPP stimulates cell growth (Ninomiya et al., 1993; Roch et al., 1992;Saitoh et al., 1989; Pietrzik et al., 1998), neurite extension (Milwardet al., 1992; Ninomiya et al., 1994; Araki et al., 1991; Jin et al.,1994; Yamamoto et al., 1994; Small et al., 1994; Li et al., 1997),neuronal survival (Mattson et al., 1995; Yamamoto et al., 1994; Furukawaet al., 1996b; Barger et al., 1995), and protects neurons from varioustoxic insults (including glucose and/or oxygen deprivation, gp120,glutamate, AP) (Mattson et al., 1993a; Mattson et al., 1993b; Barger andMattson, 1996; Guo et al., 1998b). The biochemical and cellular eventsunderlying those in vitro activities have not been elucidated yet,however it appears that sAPP function is probably carried out byreceptor mediated mechanisms and activation of a signal transductioncascade. Binding sites for sAPP were found on the surface ofneuroblastoma cells, and the binding affinity was in the same range ofoptimal concentration (10 nM) for neurite outgrowth (Ninomiya et al.,1994; Jin et al., 1994).

[0032] Depending on the target cells and the experimental paradigm, sAPPwas found to elicit various cellular responses that include activationof potassium channels (Furukawa et al., 1996a), activation of a membraneassociated guanylate cyclase (Barger and Mattson, 1995), induction ofNF-kappa B dependent transcription (Barger and Mattson, 1996), increasein phosphatidyl inositol turnover (Jin et al., 1994), and changes in thephosphotyrosine balance (Wallace et al., 1997b; Wallace et al., 1997a;Saitoh et al., 1995; Mook-Jung and Saitoh, 1997). Specifically, it wasfound that SAPP neurite extension activity on neuroblastoma wasstimulated by genistein, a tyrosine kinase inhibitor, whileorthovanadate, a phosphotyrosine phosphatase inhibitor, abolished sAPPeffects (Saitoh et al., 1995). This suggests that tyrosinedephosphorylation is involved in sAPP action. On the other hand, in adifferent experimental paradigm, sAPP was shown to activate tyrosinephosphorylation (Wallace et al., 1997b; Wallace et al., 1997a; Mook-Jungand Saitoh, 1997), which could be the result of either inhibition of atyrosine phosphatase, or activation of a tyrosine kinase. In any event,it is clear that sAPP modulates the balance of intracellularphosphotyrosine content. These in vitro activities are reflected in vivoby a stabilization of synaptic structures in the brain (Roch et al.,1994). In addition, sAPP protected brain neurons against variousinjuries (Mucke et al., 1995; Masliah et al., 1997) and providedneurological protection against ischemia in brain and spinal cord(Smith-Swintosky et al., 1994; Bowes et al., 1994; Komori et al., 1997).Most importantly, these protective and trophic activities at thecellular level are reflected at the behavioral level by memory andcognitive enhancement. Specifically, sAPP was shown to increase memoryretention in rats (Roch et al., 1994; Gschwind et al., 1996; Huber etal., 1997) and mice (Meziane et al., 1998), and conversely, compromisingthe function of sAPP resulted in memory and learning impairment (Huberet al., 1993; Doyle et al., 1990). The site of sAPP that is responsiblefor the trophic activity was mapped to a domain of 17 amino acids, fromAla319 to Met332. This peptide was shown to stimulate cell growth, tobind to neuroblastoma cells and trigger neurite extension, to enhanceneuronal survival, synaptic stability, and memory retention (Roch etal., 1994; Ninomiya et al., 1994; Jin et al., 1994; Ninomiya et al.,1993; Yamamoto et al., 1994). Furthermore, this sAPP peptide was shownto elicit the same cellular responses as sAPP itself, namely theincrease in phosphatidyl inositol turnover (Jin et al., 1994) andchanges in tyrosine phosphorylation (Saitoh et al., 1995; Mook-Jung andSaitoh, 1997). In brief, there is now mounting evidence for aneurotrophic and neuroprotective function of sAPP, which is reflected byincreased learning and memory performance.

[0033] A few years ago, two new Alzheimer genes were discovered, codingfor PS1 and PS2 (Hardy, 1997; Hardy and Gwinn-Hardy, 1998; Ray et al.,1998). These two proteins share 67% identity and although a number ofstudies report a topological structure with 6 to 9 transmembranedomains, a consensus is now emerging for a structure with 8transmembrane domains(Doan et al., 1996; Lehmann et al., 1997; Hardy,1997). Although their exact function is not known, they appear to beinvolved in intracellular protein trafficking. Thus, presenilins arepotentially implicated in APP metabolism. This hypothesis is supportedby numerous in vitro and in vivo studies showing that the AD mutationsin PS1 and PS2 alter APP metabolism resulting in elevated production ofAβ42,although the total Aβ was not changed (Duff et al., 1996; Lemere etal., 1996; Borchelt et al., 1996; Tomita et al., 1997; Ishii et al.,1997; Oyama et al., 1998; Hutton and Hardy, 1997; Cruts, VanBroeckhoven, 1998; Kim and Tanzi, 1997; Hardy, 1997; Citron et al.,1998).

[0034] The possibility that PS1 and PS2 function as APP cleaving enzymesat the y site was recently raised by a number of investigators (DeStrooper et al., 1999; Wolfe et al., 1999a; Sinha and Lieberburg, 1999;Annaert et al., 1999; Haass and De Strooper, 1999), although otherstudies suggest that the presenilins control the activity ofγ-secretase(s) rather than cleave APP directly (Murphy et al., 2000;Murphy et al., 1999). Still, the mere fact that AD mutations in proteinsother than APP itself also result in increased production of Aβ42 is acompelling argument in favor of the amyloid hypothesis. Additionally,mutations in PS1 and PS2 have been shown to be neurotoxic through anapoptotic mechanism that is independent of amyloid production, notablythe generation of superoxide and disruption of calcium homeostasis (Vitoet al., 1996; Wolozin et al., 1996; Zhang et al., 1998; Renbaum andLevy-Lahad, 1998; Guo et al., 1998b; Mattson, 1997b; Guo et al., 1999a;Guo et al., 1999b; Guo et al., 1996). Recent studies have shown that thepresenilins bind to several proteins of the Armadillo family, includingβ-catenin, δ-catenin, and p0071(Yu et al., 1998; Murayama et al., 1998;Zhou et al., 1997a; Levesque et al., 1999; Tanahashi and Tabira, 1999;Stahl et al., 1999). The biological significance of these interactionsis not clear, although recent studies suggest that FAD presenilinmutations disrupt the normal interaction pattern of the Armadilloproteins, and lead neuronal apoptosis (Zhang et al., 1998; Tesco et al.,1998). For example, the presence of PS1 and β-catenin in the samecomplex could influence the ultimate fate of β-catenin and itsinvolvement with axin, GSK3-β, and PP2A in the wingless signalingpathway (Nakamura et al., 1998; Kosik, 1999; Dierick and Bejsovec,1999). Conceivably, FAD associated mutations in PS1 could disrupt thePS1-β-catenin complex, resulting in aberrant β-catenin mediatedsignalling and eventual neuronal death.

[0035] In brief, there is now growing evidence that APP metabolism andAβ generation are central events to AD pathogenesis, and that mutationsin the presenilins can induce neuronal apoptosis as well as stimulateamyloid deposition. However, many obscure points remain. Although acandidate β-3-secretase enzyme has been identified (BACE), its normalphysiological substrate is not known. The is same statement is also truefor the γ-secretase: although PS1 and PS2 are strong candidates for theidentity of γ-secretase, it remains the be determined if they functionas catalytic or regulatory components of the γ-secretase complex, andwhat is their natural physiological substrate. Even less is known aboutthe α-secretase, the enzyme that cleaves APP at the α site and thusprecludes Aβ formation. The proteins that mediate the neurotrophic andneuroprotective effects of sAPP are unknown. This last point is ofutmost importance because an alteration of APP metabolism could resultin both the generation of a toxic product (Aβ) and the impairment ofsAPP trophic activity (Saitoh et al., 1994; Roch et al., 1993; Saitohand Roch, 1995). In this respect, it is interesting that one APPmutation associated with Alzheimer's results in a defective neuriteextension activity of sAPP (Li et al., 1997). Moreover, the balance ofphosphorylation cascades is deeply altered in Alzheimer brains (Saitohand Roch, 1995; Jin and Saitoh, 1995; Mook-Jung and Saitoh, 1997; Saitohet al., 1991; Shapiro et al., 1991). Because hyperphosphorylation of themicrotubule-associated protein τ is necessary for the formation ofpaired helical filaments and tangles, a disruption of thephosphorylation cascade could be the link between the amyloid and the τpathways.

[0036] Proteins that interact with sAPP are expected to be involved inits biological function, including neuron survival, synaptic formationand stability, learning and memory. Thus, it is expected that some ofthese will become promising targets for drugs designed to tackle AD anda number of other neurodegenerative conditions. Because sAPP showedobvious protective effects in ischemia models (Smith-Swintosky et al.,1994; Bowes et al., 1994; Mattson, 1997c; Komori et al., 1997), it isreasonable to assume that drugs that mimic sAPP function could be usedto alleviate the effects of stroke (Mattson, 1997c). Likewise, thediscovery of new proteins that interacts with the presenilins,δ-catenin, Fe65, or axin could establish previously unknown biochemicalpathways, and identify drug targets that could influence APP metabolism,presenilin functions, neuronal survival, and synaptic maintenance. Asmentioned above, cholinergic neurons are particularly affected andlevels of acetylcholine are markedly reduced in AD brains compared tocontrols. To date, the only Alzheimer drugs available are inhibitors ofacetylcholine esterase (AChE). This enzyme has also been found to beassociated with neuritic plaques (Inestrosa and Alarcon, 1998) and tointeract with APP (Alvarez et al., 1998). Thus, proteins that interactwith AChE also represent important opportunities for drug discovery inAlzheimer's disease.

[0037] According to the present invention, new protein-proteininteractions have been discovered. The discovery of these interactionshas identified several protein complexes for each protein-proteininteraction. The protein complexes for these interactions are set forthbelow in Tables 1-33, which also identify the new protein-proteininteractions of the present invention. The involvement of theprotein-protein interactions in neurodegenerative disease is describedbelow with reference to individual or grouped interactions. TABLE 1Protein Complexes of BAT3-Glypican Interaction HLA-B associatedtranscript (BAT3) and glypican A fragment of BAT3 and glypican BAT3 anda fragment of glypican A fragment of BAT3 and a fragment of glypican

[0038] TABLE 2 Protein Complexes of BAT3-LRP2 Interaction HLA-Bassociated transcript (BAT3) and LRP2 A fragment of BAT3 and LRP2 BAT3and a fragment of LRP2 A fragment of BAT3 and a fragment of LRP2

[0039] TABLE 3 Protein Complexes of BAT3-LRPAP1 Interaction HLA-Bassociated transcript (BAT3) and LRPAP1 A fragment of BAT3 and LRPAP1BAT3 and a fragment of LRPAP1 A fragment of BAT3 and a fragment ofLRPAP1

[0040] TABLE 4 Protein Complexes of BAT3-Transthyretin Interaction HLA-Bassociated transcript (BAT3) and transthyretin A fragment of BAT3 andtransthyretin BAT3 and a fragment of transthyretin A fragment of BAT3and a fragment of transthyretin

[0041] TABLE 5 Protein Complexes of Fe65-PN7740 Interaction Fe65 andPN7740 A fragment of Fe65 and PN7740 Fe65 and a fragment of PN7740 Afragment of Fe65 and a fragment of PN7740

[0042] TABLE 6 Protein Complexes of Mint1-GS Interaction Mint1 andglutamine synthase (GS) A fragment of Mint1 and GS Mint1 and a fragmentof GS A fragment of Mint1 and a fragment of GS

[0043] TABLE 7 Protein Complexes of Mint1-KIAA0427 Interaction Mint1 andKIAA0427 A fragment of Mint1 and KIAA0427 Mint1 and a fragment ofKIAA0427 A fragment of Mint1 and a fragment of KIAA0427

[0044] TABLE 8 Protein Complexes of PS1-Mint1 Interaction Presinilin 1(PS1) and Mint1 A fragment of PS1 and Mint1 PS1 and a fragment of Mint1A fragment of PS1 and a fragment of Mint1

[0045] TABLE 9 Protein Complexes of CASK-Dystrophin Interaction CASK anddystrophin A fragment of CASK and dystrophin CASK and a fragment ofdystrophin A fragment of CASK and a fragment of dystrophin

[0046] TABLE 10 Protein Complexes of CIB-S1P Interaction CIB and S1P Afragment of CIB and S1P CIB and a fragment of S1P A fragment of CIB anda fragment of S1P

[0047] TABLE 11 Protein Complexes of Mint2-S1P Interaction Mint2 and S1PA fragment of Mint2 and S1P Mint2 and a fragment of S1P A fragment ofMint2 and a fragment of S1P

[0048] TABLE 12 Protein Complexes of PS1-P-glycerate DH InteractionPresinilin 1 (PS1) and P-glycerate DH A fragment of PS1 and P-glycerateDH PS1 and a fragment of P-glycerate DH A fragment of PS1 and a fragmentof P-glycerate DH

[0049] TABLE 13 Protein Complexes of PS1-Beta-ETF Interaction Presinilin1 (PS1) and beta-ETF A fragment of PS1 and beta-ETF PS1 and a fragmentof beta-ETF A fragment of PS1 and a fragment of beta-ETF

[0050] TABLE 14 Protein Complexes of PS1-GAPDH Interaction Presinilin 1(PS1) and GAPDH A fragment of PS1 and GAPDH PS1 and a fragment of GAPDHA fragment of PS1 and a fragment of GAPDH

[0051] TABLE 15 Protein Complexes of PS2-GAPDH Interaction Presinilin 2(PS2) and GAPDH A fragment of PS2 and GAPDH PS2 and a fragment of GAPDHA fragment of PS2 and a fragment of GAPDH

[0052] TABLE 16 Protein Complexes of CIB-ATP synthase Interaction CIBand ATP synthase A fragment of CIB and ATP synthase CIB and a fragmentof ATP synthase A fragment of CIB and a fragment of ATP synthase

[0053] TABLE 17 Protein Complexes of KIAA0443-PI-4-kinase InteractionKIAA0443 and PI-4-kinase A fragment of KIAA0443 and PI-4-kinase KIAA0443and a fragment of PI-4-kinase A fragment of KIAA0443 and a fragment ofPI-4-kinase

[0054] TABLE 18 Protein Complexes of KIAA0443-5HT-2A R InteractionKIAA0443 and serotonin receptor 2A (5HT-2A R) A fragment of KIAA0443 and5HT-2A R KIAA0443 and a fragment of 5HT-2A R A fragment of KIAA0443 anda fragment of 5HT-2A R

[0055] TABLE 19 Protein Complexes of KIAAO35 1-TRIO Interaction KIAA0351and TRIO A fragment of KIAA0351 and TRIO KIAA0351 and a fragment of TRIOA fragment of KIAAO351 and a fragment of TRIO

[0056] TABLE 20 Protein Complexes of CIB-MILK2 Interaction CIB and MLK2A fragment of CIB and MLK2 CIB and a fragment of MLK2 A fragment of CIBand a fragment of MLK2

[0057] TABLE 21 Protein Complexes of BAX-slo K⁺ channel Interaction BAXand slo K⁺channel A fragment of BAX and slo K⁺ channel BAX and afragment of slo K⁺ channel A fragment of BAX and a fragment of slo K⁺channel

[0058] TABLE 22 Protein Complexes of FAK2-SUR1 Interaction Focaladhesion kinase 2 (FAK2) and SUR1 A fragment of FAK2 and SUR1 FAK2 and afragment of SUR1 A fragment of FAK2 and a fragment of SUR1

[0059] TABLE 23 Protein Complexes of Mint2-PDE-9A Interaction Mint2 andPDE-9A A fragment of Mint2 and PDE-9A Mint2 and a fragment of PDE-9A Afragment of Mint2 and a fragment of PDE-9A

[0060] TABLE 24 Protein Complexes of CIB-SCD2 Interaction CIB and SCD2 Afragment of CIB and SCD2 CIB and a fragment of SCD2 A fragment of CIBand a fragment of SCD2

[0061] TABLE 25 Protein Complexes of rab11-FAK Interactioncarboxy-termmal region of rab-related GIP-binding protein 11 (rab11) andfocal adhesion kinase (FAK) A fragment ofrab11 and FAK rabli and afragment of FAK A fragment ofrab11 and a fragment of FAK

[0062] TABLE 26 Protein Complexes of FAK-Casein kinase II Interactionfocal adhesion kinase (FAK) and casein kinase II A fragment of FAK andcasein kinase II FAK and a fragment of casein kinase II A fragment ofFAK and a fragment of casein kinase II

[0063] TABLE 27 Protein Complexes of FAK-GST trans. M3 Interaction focaladhesion kinase (FAX) and GST trans. M3 A fragment of FAK and GST trans.M3 FAK and a fragment of GST trans. M3 A fragment of FAK and a fragmentof GST trans. M3

[0064] TABLE 28 Protein Complexes of Bcr-PSD95 Interaction Bcr and PSD95A fragment of Bcr and PSD95 Ber and a fragment of PSD95 A fragment ofBcr and a fragment of PSD95

[0065] TABLE 29 Protein Complexes of Bcr-DLG3 Interaction Bcr and DLG3 Afragment of Bcr and DLG3 Bcr and a fragment of DLG3 A fragment of Bcrand a fragment of DLG3

[0066] TABLE 30 Protein Complexes of Bcr-Semaphorin F Interaction Bcrand semaphorin F A fragment of Bcr and semaphorin F Bcr and a fragmentof semaphorin F A fragment of Bcr and a fragment of semaphorin F

[0067] TABLE 31 Protein Complexes of Bcr-HTF4A Interaction Bcr and HTF4AA fragment of Bcr and HTF4A Bcr and a fragment of HTF4A A fragment ofBcr and a fragment of HTF4A

[0068] TABLE 32 Protein Complexes of Bcr-SRCAP Interaction Bcr and SRCAPA fragment of Bcr and SRCAP Bcr and a fragment of SRCAP A fragment ofBcr and a fragment of SRCAP

[0069] TABLE 33 Protein Complexes of PSD95/PN7740 Interaction PSD95 andPN7740 A fragment of PSD95 and PN7740 PSD95 and a fragment of PN7740 Afragment of PSD95 and a fragment of PN7740

[0070] APP metabolism is a critical event in the pathogenesis ofAlzheimer's, because it leads to the release of either toxic (Aβ) ortrophic (sAPP) metabolites(Cummings et al., 1998; Roch and Puttfarcken,1996). In this respect, it is very important to identify proteinsinvolved in the intracellular trafficking of APP. Proteins that interactwith the cytosolic C-terminal region of APP play a major role in thisprocess. The interaction of APP with Fe65, with Fe65 L, with Mint1, andwith Mint2 have been well documented (Russo et al., 1998; Sastre et al.,1998). We also described an interaction between APP and BAT3, andbetween BAT3 and δ-adaptin, and we have explained the importance ofthese interactions in APP trafficking and metabolism (see U.S. patentapplication No. Ser. 09/466,139; International Patent Application No.PCT/US99/30396 (WO 00/37483)), filed Dec. 21, 1999,). The presenilins(PS1and PS2) are also involved in AD pathogenesis. Mutations in PS1 andPS2 are known to cause AD (Hardy, 1997; Selkoe, 1998), and recently, itwas found that the presenilins could be the γ-secretase that cleave APPat the C-terminus of the Aβ peptide (Wolfe et al., 1999b; De Strooper etal., 1999; Wolfe et al., 1999a; Li et al., 2000a; Li et al., 2000b). PS1interacts with δ-catenin (Zhou et al., 1997a; Tanahashi and Tabira,1999) and CIB interacts with both PS1 and PS2 (Stabler et al., 1999). Toextend our understanding of the role of these proteins in APPtrafficking and metabolism, we have used some of the proteins mentionedabove as baits in yeast two-hybrid searches.

[0071] Using a fragment of BAT from amino acids 271 to 480 as a bait ina yeast two-hybrid search, we found a clone encoding amino acids 400 to483 of glypican as a prey. Glypican is one of the several core proteinsof heparan sulfate proteoglycan (other core proteins include the variousforms of syndecan, perlecan, appican, and others). The glypican cDNAcodes for 558 residues, but after removal of the signal peptide (aa 1 to23) and of the propeptide (aa 531 to 558), the mature form of glypicancontains 507 amino acids. Glypican is attached to the membrane through aGPI anchor and was recently shown to be a receptor that mediates Abtoxicity (Schulz et al., 1998). On the other hand, secreted glypicanbinds to substrate-bound APP and inhibits neurite extension normallyelicited by APP (Williamson et al., 1996). The mechanism of inhibitionmay be a competition of glypican for substrate-bound APP, against otherendogenous proteoglycans that are normally required for APP to stimulateneurite outgrowth. In addition, because glypican bears heparan sulfateand because heparin stimulates β-secretase (Leveugle et al., 1997),glypican could favor release of sAPPβ vs sAPPα from cells, thus reducingthe trophic potency of sAPP (sAPPβ is known to have greatly reducedneurite extension (Li et al., 1997) and neuroprotective (Furukawa etal., 1996b) activities compared to aAPPα). Thus, BAT3 interacts withboth APP and glypican, which are known to interact with each other andcontrol phenomenon such as neurite extension and neuronal survival.Pharmacological modulation of the BAT3-glypican interaction mightinfluence the neurotrophic effects elicited by APP, as well as theneurotoxic effects mediated by Aβ.

[0072] Using a fragment of BAT3 from amino acids 740 to 1040 as a baitin a yeast two-hybrid search, we found a clone encoding amino acids 1 to304 of LRP2 (LDL receptor related protein 2) as a prey. This protein(also called glycoprotein 330 and megalin) was shown to bind ApoJ(Kounnas et al., 1995), as well as ApoE (Orlando et al., 1997). A recentstudy (Zlokovic et al., 1996) suggested that LRP2 is necessary for thetransport of ApoJ and ApoJ-Aβ1-40 complexes across the blood brainbarrier, into the brain parenchyma. Another investigation (LaFerla etal., 1997) showed that intracellular accumulation of ApoE is correlatedwith the presence of intracellular Aβ in the same cytoplasmic granules,suggesting that uptake of lipids may have stabilized the hydrophobic Aβprotein within the cell. This work suggested a role for LRP2 in the ApoEuptake. Thus, LRP2 appears to be involved in the transport andstabilization of the Aβ protein. In this respect, the interactions ofBAT3 with APP and LRP2 generates a biochemical link between APP andLRP2. We suggest that pharmacological modulation of the BAT3-LRP2interaction might influence the transport and stabilization of the Aβprotein.

[0073] Using the same BAT3 bait, we also found a clone encoding aminoacids 11 to 361 of LRPAP1 (LRP associated protein 1) as a prey. Thisprotein was first isolated as a 39 kDa component of the alpha2-macroglobulin (A2M) receptor complex (Striekland et al., 1991) and wascalled A2MRAP (for A2M receptor-associated protein), or MRAP, or simplyRAP. Further studies (Korenberg et al., 1994; Van Leuven et al., 1995;Willnow et al., 1996; Willnow et al., 1995) showed that the human RAPgene (LRPAP1) is on chromosome 4p16.3. RAP, which is predominantly foundin the endoplasmic reticulum, binds LRP1 and LRP2 and functions as achaperone protein that selectively protects endocytic receptors (such asLRPs) by binding to newly synthesized receptor polypeptides, therebypreventing ligand-induced aggregation and subsequent degradation in theER. In the light of the interaction between BAT3 and LRP2 (describedabove), it is important to note that A2M (a ligand for LRP1 and LRP2)binds to the Aβ domain of APP (Hughes et al., 1998). Thus, our findingsuggest that BAT3 is an adaptor molecule that brings together APP andthe components of the LRP-RAP-A2M complexes. A recent study has shownthat ligand binding to receptor of the LDL receptor family triggers notonly receptor internalization, but initiates a signal transductioncascade (Trommsdorff et al., 1998). Proteins such as Fe65 and DAB bindto the cytoplasmic tails of LRP, the LDL receptor, and APP, where theycan potentially serve as molecular scaffolds for the assembly ofcytosolic multiprotein complexes. The interaction pattern of BAT3 (withAPP, LRP2, and LRPAP1) suggests a similar role. We suggest thatpharmacological modulation of the BAT3-LRP2 and BAT3-LRPAP1 interactionsmight affect the signal transduction cascade elicited by these receptormolecules, and in turn, control APP trafficking and metabolism.

[0074] Using the same BAT3 bait, we also found a clone encoding aminoacids 7 to 148 of transthyretin (TTH) as a prey. TTH is responsible forthe transport of the thyroid hormone thyroxine from the bloodstream tothe brain, is very abundant in the CSF (25% of total CSF protein) and,in the central nervous system, is synthesized exclusively by theepithelial cells of the choroid plexus. The active form is ahomotetramer. Even before the identification of the Aβ protein, TTH wasidentified as a component of the neuritic plaques, neurofibrillarytangles, and cerebral vessel amyloid deposits (Shirahama et al., 1982).More recent studies have shown that TTH levels are reduced in the CSF ofAD patients compared to age-matched controls (Merched et al., 1998), andTTH binding to Aβ inhibits amyloid fibrils in vitro (Schwarzman et al.,1994). Numerous variants in the transthyretin sequence are associatedwith various forms of amyloid polyneuropathy. Except for blood vessels,amyloid deposits are never found in the CNS. The interactions of BAT3with APP, δ-adaptin (a lysosome targeting protein (see U.S. patentapplication Ser. No. 09/466,139; International Patent Application No.PCT/US99/30396 (WO 00/37483)), glypican (a mediator of Aβtoxicity, seeabove), LRP2 (transport and stabilization of the Aβ protein, see above),and now with TTH suggest a close involvement of BAT3 in AD pathogenesis.Similarly to the BAT3-LRP2 interaction, we suggest that pharmacologicalmodulation of the BAT3-TTH interaction might influence the transport andstabilization of the Aβ protein.

[0075] Using a fragment of FE65 from amino acids 360 to 552 as a bait(the first phosphotyrosine binding domain, PTB), we found 3 clonescoding for a novel protein. These clones have a coding capacity of 289amino acids and contain stop codons in the other two reading frames.Sequence analysis of the novel protein fragment revealed the presence ofa domain with high similarity to phosphatase 2C, from amino acids 78 to289 of our insert. Using a variety of methods (RACE, arrayed libraryscreening, plaque lifts), we extended the sequence of the cDNA encodingthe novel protein, and found sequence containing a open reading frame(ORF) coding for 372 amino acids. The putative ATG initiation codon ispreceded by a purine (G) residue in position -3, and by several upstreamSTOP codons, suggesting that it represents the authentic initiationcodon. At the end of the 3′ UTR (untranslated region), we found acanonical polyadenylation signal (AATAAA) shortly before the poly Aitself. The phosphatase 2C domain of the novel protein, which we namedPN7740, is from amino acids 104 to 339 Thus, we have identified a novelphosphatase that binds to the first PTB domain of Fe65. This is veryimportant because the balance of β-secretion vs α-secretion of APP isregulated by phosphorylation (Farber et al., 1995; Caporaso et al.,1992; Buxbaum et al., 1990; Buxbaum et al., 1993; Sabo et al., 1999). Wesuggest that this balance can be modified by the pharmacologicalmodulation of the interaction between Fe65 and the novel phosphatase, orby the direct pharmacological modulation of the activity the novelphosphatase itself. It is also possible that this novel phosphatasemodulates the phosphorylation status of proteins involved in APPmetabolism, such as PS1, PS2, and nicastrin. We have submitted thenucleotide and aminoacid sequences of the PN7740 cDMA and protein in aseparate patent application. These sequences are added in the appendixof the present application for reference.

[0076] The Mint1 protein (also called X11 alpha) is a cytosolic proteinthat interacts that the C terminal fragment of APP. Mint1 contains a PTBdomain and a PDZ domain. Interaction of Mint1 with APP increases thelevels of cellular APP and reduces the levels of both α-and β-secretedforms of APP (Borg et al., 1998b). The mechanism by which Mint1 affectsAPP metabolism is not clear at this point. Using a fragment of Mint1from amino acids 447 to 758 as a bait in a yeast two-hybrid search, wefound a clone encoding amino acids 364 to 589 of KIAA0427 as a prey. TheKDRI (Kazusa DNA Research Institute) database reports the sequence of afull-length clone for this protein, coding for 598 aa. No wellcharacterized protein domain was identified in KIAA0427 and thus itsfunction is unknown. Therefore, for all practical purpose, we considerthis protein as functionally novel, although its sequence is not new.The mRNA for KIAA0427 is found at very high levels message in brain,medium levels in lung, kidney, prostate, testis, and ovary, and lowlevels in all other tissues examined. We suggest that KIAA0427 mediatesthe effect of Mint 1 on APP metabolism and that pharmacologicalmodulation of the Mint1-KIAA0427 interaction might influence APPsecretion.

[0077] Additional evidence for the role of Mint1 in APP metabolism comesfrom its interaction with PS1. Using a fragment of PS1 from amino acids1 to 91 as a bait in a yeast two-hybrid search, we found a cloneencoding amino acids 470 to 821 of Mint1 as a prey. This domain containsmost of the PTB domain (amino acids 457 to 643) which is known to bindthe cytoplasmic domain of APP. Thus, PS1 and APP might compete for thePTB domain of Mint1 and FAD associated mutations in PS1 are expected toalter its interaction with Mint1. We suggest pharmacological modulationof the PS1-Mint1 interaction might influence APP metabolism and amyloidproduction.

[0078] Using a fragment of Mint1 from amino acids 739 to 857 as a baitin a yeast two-hybrid search, we found a clone encoding amino acids 45to 212 of glutamine synthetase as a prey (GS, also called glutamateammonia ligase). This enzyme catalyzes the ATP-dependent conversion ofL-glutamate and NH3 to glutamine. In the brain, GS is secreted byastrocytes and plays a crucial role in the clearance of excitotoxicglutamate released in synapses. GS concentration is dramaticallyincreased in the CSF from AD patients (Gunnersen and Haley, 1992). Thisphenomenon could be a defense mechanism against glutamateexcitotoxicity, reflecting astrogliosis rather than an Alzheimerspecific phenomenon. It is striking that the Aβ peptide interacts withGS and inhibits its activity by oxidative modification (Aksenov et al.,1997). Thus, the inactivation of GS by Aβ could lead to elevatedconcentration of excitotoxic glutamate. Furthermore, a previous study bythe same group (Aksenov et al., 1996) showed that Aβ-mediatedinactivation of GS is accompanied by the loss of immunoreactive GS and aconcomitant significant increase of Aβ neurotoxicity. The interactionbetween GS and Mint1 suggests that Mint1 may act as an adapter molecule,bringing GS into a complex with APP. It is thus possible that Mint1favors the oxidation of GS by Aβ, with the concomitant elevation insynaptic glutamate concentration. We suggest that pharmacologicalmodulation of the Mint1-GS interaction could reduce its oxidation by Aβand thus keep glutamate concentration below toxic levels.

[0079] CASK is a postsynaptic protein of the MAGUK family, whichcontains a PDZ domain, an SH3 domain, a guanylate kinase domain, and acalmodulin-binding domain. It interacts with Mint1, with APP, and withthe neurexins (Borg et al., 1998a; Borg et al., 1999). Using a fragmentof CASK from amino acids 306 to 574 as a bait in a yeast two-hybridsearch (calmodulin-binding domain and its PDZ domain), we found a cloneencoding amino acids 909 to 1280 of dystrophin as a prey. This proteinis largely known for its involvement in Duchenne muscular dystrophy(Hoffman, 1999), and was recently localized in post-synaptic densitiesin rat brain (Kim et al., 1992). Reciprocally, PSD-95 and DLG2 (PSD-93)(Rafael et al., 1998) as well as APP (Askanas et al., 1992) are alsofound at neuromuscular junctions, where they participate in theclustering of nicotinic acetylcholine receptors, a phenomenon that alsorequires dystrophin (Kong and Anderson, 1999). The interaction ofdystrophin with CASK, together with its localization in brainpost-synaptic densities suggest that this protein (and most probablyproteins from the dystrophin associated complex, like syntrophin) isanother component of the synaptic cytoskeletal structure. Interestingly,both APP and dystrophin are found (often with gelsolin) in thepathological features of several neuromuscular diseases (De Bleecker etal., 1996; Nonaka, 1994). We suggest that adequate pharmacologicalmodulation of the CASK-dystrophin interaction might help prevent thebrain or neuromuscular synaptic degeneration observed in manyneuropathological conditions.

[0080] CIB is a calcium-binding protein that we found to interact withFKBP25, which is itself a PS1 interactor (see U.S. patent applicationSer. No. 09/466,139; International Patent Application No. PCT/US99/30396(WO 00/37483)). Based on its sequence similarity with calcineurin B, CIBwas proposed to be the regulatory subunit of a yet-to-be-discoveredcalcium-activated phosphatase (Naik et al., 1997). In our previouspatent application, we have suggested that this novel putativephosphatase might control the activity of the ryanodine receptor, andthus calcium homeostasis. Recently CIB was found to also interact withPS2 and PS1 (Stabler et al., 1999). Because of the causal role of PS1and PS2 mutations in Alzheimer's disease, proteins that interact withCIB are likely to play a major role in AD pathogenesis. Mint2 (alsocalled X11 beta) is a cytosolic protein that interacts that theC-terminal fragment of APP (Tomita et al., 1999). Mint2 contains a PTBdomain and two PDZ domains. In addition to the cytosolic fragment ofAPP, Mint1 and Mint2 both bind Munc-18 and are involved in the fusion ofsynaptic vesicles with the presynaptic membrane (Okamoto and Sudhof,1997; Okamoto and Sudhof, 1998). Thus, the Mints proteins play a role inAPP trafficking and synaptic function. Proteins that associate with theMints are therefore likely to be involved in AD pathogenesis. Moreover,proteins that associate with CIB and with Mint1 or Mint2 are even morelikely to play a central role in AD development. Thus, we used CIB andthe Mints proteins as a bait in a yeast two-hybrid search, and we founda prey protein, SIP, that binds to CIB and Mint2.

[0081] S1P is a transmembrane protease that catalyzes the first cleavagestep of the SREBPs (sterol regulatory element-binding proteins)processing (Sakai et al., 1998). SREBPs are membrane-bound transcriptionfactors that activate genes for enzymes involved in cholesterol andfatty acids biosynthesis (Brown and Goldstein, 1999). Two sequentialcleavage steps are necessary to release the active N-terminal domain ofSREBPs from endoplasmic reticulum (ER) membranes and for the subsequenttargeting of this protein domain to the nucleus. The first step iscatalyzed by a protein called SIP (Site 1 Protease) which cleaves SREBPsin the ER luminal domain, while the second step is catalyzed by S2P(Site 2 Protease) which cleaves SREBPs in the first transmembrane domain(Rawson et al., 1997; Ye et al.2000). This process is controlled by theSREBP cleavage-activating protein (SCAP), a large regulatory proteinwith eight transmembrane domains that acts as a sterol sensor and isnecessary for the activation of the SIP protease (Nohturfft et al.,1999). This protein is also known as SKI-1. In addition to SREBPs,S1P/SKI-1 also cleaves the proBDNF molecule into its active form (Seidahet al., 1999b), and belongs to the subtilisin/kexin family of precursorconvertases (Seidah et al., 1999a). Because CIB interacts with both PS1and PS2, and because Mint2 interacts with APP, S1P might be involved inAPP processing. It appears unlikely that SIP is the γ-secretase (sinceit does not cleave in the transmembrane domain but in the luminaldomain), and there is now mounting evidence that PS1 could be theγ-secretase (Wolfe et al., 1999b; Selkoe and Wolfe, 2000; Li et al.,2000a; Li et al., 2000b), although this is still controversial (Murphyet al., 2000; Murphy et al., 1999). Recently, two novel enzymes withβ-secretase activity have been identified as BACE and BACE-like (Vassaret al., 1999; Hussain et al., 1999; Yan et al., 1999). It is thusunlikely that S 1P represent yet a third enzyme with β-secretaseactivity. However, we favor the possibility that S1P might be anα-secretase. Although the exact site of APP α-cleavage is immediatelyafter the Lys16 residue of the Aβ peptide (Anderson et al., 1991),mutational analyses have shown that α-secretase has poor sequencespecificity (substitution of Lys16 by a Gly, Leu, Thr, Arg, or Metresidue did not affect cleavage) (Sisodia, 1992)but cleaves at adistance about 12 to 13 residues away from the membrane. Interestingly,the cleavage of SREBP2 by S1P occurs immediately after the Leu522residue, which is 12 residues before the second transmembrane domain(Duncan et al., 1997). Additionally, it is also remarkable that S1Pactivity regulates (and is regulated by) cholesterol levels (Brown andGoldstein, 1999). Raised cholesterol levels reduce the α-secretion ofAPP (Bodovitz and Klein, 1996). Conceivably, high cholesterol levelscould lower S1Pactivity, thus reducing APP α-secretion. In brief, wehave identified a transmembrane protease, S1P , that interacts with CIBand Mint2, that might be involved in APP metabolism, and that showsseveral important features expected from a putative α-secretase. Wesuggest that adequate pharmacological modulation of S1Pactivity orinteraction with CIB or Mint2 might shift the metabolism of APP towardthe α-secretase pathway.

[0082] There is a growing body of evidence that disruption of energymetabolism is an important factor in neurodegenerative disorders,including Alzheimer's Disease (Beal, 1998; Nagy et al., 1999; Rapoportet al., 1996). Mitochondrial dysfunctions result in low ATP levels andproduction of free oxiradicals that are extremely toxic to neurons(Simonian and Coyle, 1996; Beal, 1996). In Alzheimer's, FAD mutations inPS1 have been shown to trigger neuronal apoptosis through a mechanisminvolving the disruption of mitochondrial function, energy metabolism,and calcium homeostasis (Guo et al., 1998a; Guo et al., 1999a; Mattsonet al., 2000; Begley et al., 1999). To gain further insight into theinvolvement of mitochondrial function and energy metabolism in ADpathogenesis, we used the presenilins (PS1 and PS2) as well as theircommon interactor CIB (Stabler et al., 1999) as baits in yeasttwo-hybrid searches and looked for interactors that are eithermitochondrial proteins, or that are involved in energy metabolism. Wefound an interaction between PS-1 and α-enolase, a glycolytic enzymewhich transforms 2-phosphoglycerate into phosphoenol pyruvate, and isthus directly involved in energy production (see U.S. patent applicationSer. No. 09/466,139; International Patent Application No. PCT/US99/30396(WO 00/37483)).

[0083] In addition, we found an interaction between PS1 andphosphoglycerate dehydrogenase (P-glycerate DH). This enzyme isresponsible for the oxidation of 3-phosphoglycerate, a glycolysisintermediate, to 3-phosphohydroxypyruvate, an intermediate of the serinebiosynthetic pathway. We also found that both PS1 and PS2 interact withglyceraldehyde-3-phosphate dehydrogenase (GAPDH). This enzyme catalyzesthe oxidation of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate,with the concomitant reduction of NAD+to NADH. In addition to its rolein glycolysis, GAPDH is also directly involved in neuronal apoptosis(Chen et al., 1999) and its role in AD pathogenesis is strengthened byits interaction with the cytosolic domain of APP (Schulze et al., 1993).In brief, GAPDH is a central molecule that interacts with all threemajor Alzheimer proteins (PS1, PS2, and APP), mediates neuronalapoptosis, and is involved in energy metabolism.

[0084] We also found that PS1 interacts with the beta subunit of theelectron transfer flavoprotein (beta-ETF). This protein is an electronacceptor for several dehydrogenases and transfers electrons to the mainrespiratory electron transport chain. A disruption of the interactionbetween PS1 and the electron transfer flavoprotein (possibly caused byFAD mutations) might alter normal mitochondrial function and energyproduction and thus threaten neuronal survival. We also found aninteraction between CIB and the beta subunit of ATP synthase. CIB is acalcium-binding protein that interacts with both PS1 and PS2 (Stabler etal., 1999), and with FKBP25, another PS1 interactor that might also beinvolved in the regulation of calcium homeostasis (see U.S. patentapplication Ser. No. 09/466,139; International Patent Application No./US99/30396, (WO 00/37483)). These five interactions reported here linkPS1, PS2, and CIB to proteins involved in mitochondrial function andenergy metabolism, two cellular processes that are severely affected inAlzheimer's and other neurodegenerative diseases. We suggest thatadequate pharmacological modulation of these interactions or modulationof the enzymatic activities of the identified preys might prevent theneuronal degeneration observed in AD.

[0085] Intracellular calcium is stored mainly inside the endoplasmicreticulum (ER), and is released into the cytosol upon activation of theryanodine receptor or the inositol-triphosphate (IP3) receptor, two ERtransmembrane proteins. The fine regulation of the activity of these tworeceptors is crucial for the control of calcium homeostasis, and thusfor neuronal survival (Mattson and Furukawa, 1996). A number of studiessuggest that disruption of calcium homeostasis underlies Aβneurotoxicity (Mattson, 1994; Joseph and Han, 1992; Mattson et al.,1993a; Guo et al., 1998b). In addition to their role in the productionof Aβ42, the presenilins are also known to participate in the control ofcalcium homeostasis through the regulation of calcium release frominternal stores (Mattson et al., 1998; Mattson et al., 1999). Alzheimerassociated mutations in the presenilins have been shown to disrupt thiscontrol, leading to neuronal apoptosis (Guo et al., 1998b; Guo et al.,1996). PS1 was shown to interact with δ-catenin (Guo et al., 1998b; Guoet al., 1996), but the functional significance of this interaction hasremained elusive. We have found that δ-catenin interacts with KIAA0443,a protein that contains a lipocalin domain and is thus probably involvedin the transport of small lipophilic molecules (U.S. patent applicationSer. No. 09/466,139; International Patent Application No. PCT/US99/30396(WO 00/37483)).

[0086] Using KIAA0443 as a bait in a yeast two-hybrid search, we foundthe enzyme phosphatidylinositol-4 kinase (PI-4 kinase) as a prey. Thisenzyme catalyzes the first commited step in the biosynthesis of IP3. Itwas reported to be expressed mainly in brain and placenta (Wong andCantley, 1994). It contains several biologically active domains,including an ankyrin repeat domain, a lipid kinase unique domain, apleckstrin homology domain, a presumed lipid kinase/protein kinasehomology domain, a proline-rich region, and an SH3 domain (Nakagawa etal., 1996). The interaction of KIAA0443 with PI-4 kinase and thepresence of a lipocalin domain in KIAA0443 suggest that KIAA0443 mightbring a lipid such as phosphatidylninositol in close proximity of thekinase that phosphorylates it. The regulation of this process, leadingto the formation of IP3, is obviously important for the control ofcalcium homeostasis. Because KIAA0443 interacts with δ-catenin, itself aPS1 interactor, it is possible that PS1 mutations associated withAlzheimer's disrupt the interaction network that includes PS1,δ-catenin, KIAA 0443, and PI-4 kinase. This in turn could lead to analteration of PI-4 kinase activity, resulting in abnormal levels of IP3and disruption of calcium homeostasis. We suggest that pharmacologicalmodulation of PI-4 kinase activity or modulation of the protein-proteininteractions connecting this enzyme with PS1 (via KIAA0443 andδ-catenin) might prevent the disruption of calcium homeostasis and theresulting neuronal apoptosis.

[0087] In the same search with KIAA0443 as a bait, we found theserotonin receptor 2A (5HT-2AR) as a prey. Interestingly, the 5HT-2A and5HT-2C receptors stimulate APP α-secretion, thus precluding Aβ formation(Nitsch et al., 1996). Moreover, the serotonin derivativeN-acetylserotonin and melatonin were shown to improve cognition andprotect neurons from Aβ toxicity (Bachurin et al., 1999). These findingssuggest that 5HT-2AR agonists might prevent amyloid formation as well asprotect neurons from Aβ peptide already present. KIAA0443 appears tolink the δ-catenin network (which includes the presenilins) to theserotoninergic system, thus opening a novel promising therapeuticavenue. We suggest that pharmacological modulation of the 5HT-2AR andits interaction with KIAA0443 might prevent amyloid formation and mightprotect neurons from Aβ toxicity.

[0088] We previously reported an interaction between APP and KIAA0351,and we suggested that this protein might mediate the neurotrophiceffects of APP through its pleckstrin homology (PH) domain and aconnection to guanine nucleotide exchange factors (GEFs) and cyclic GMP(see U.S. patent application Ser. No. 09/466,139; International PatentApplication No. PCT/US99/30396 (WO 00/37483)). Using KIAA0351 as a baitin a yeast two-hybrid search, we found the TRIO protein as a prey. TRIO,initially identified as an interactor for LAR, a transmembrane receptorwith tyrosine phosphatase activity (Debant et al., 1996), is a largeprotein (2861 aa) which contains two pleckstrin homology (PH) domains,one SH3 domain, and a protein kinase domain. All these functionaldomains are clustered in the C-terminal half of the protein.Additionally, TRIO contains two guanine nucleotide exchange factor (GEF)domains; one is rac-specific, and the other one rho-specific (Debant etal., 1996). TRIO contains an Ig-like domain (close to the kinase domainin the C-terminal region), and 4 spectrin repeats (in the N-terminalregion).

[0089] Thus, APP interacts directly with a transmembrane receptortyrosine phosphatase, PTPZ (see U.S. patent application Ser. No.09/466,139; International Patent Application No. PCT/US99/30396 (WO00/37483)), and indirectly (through the KIAA0351 and TRIO connection)with another transmembrane receptor tyrosine phosphatase, LAR. Theneurotrophic and neuroprotective effects of sAPP are well documented(Jin and Saitoh, 1995; Mattson, 1997a; Saitoh et al., 1995; Mattson etal., 1999; Mattson and Duan, 1999). In this respect, it is important tonote that Abl, TRIO, LAR, and other associated proteins are involved inaxonal development (Lanier and Gertler, 2000). A more recent study alsoshowed that downregulation of LAR activity prevents apoptosis andincreases NGF-induced neurite outgrowth (Yeo et al., 1997). Togetherwith the recent observation that pleiotrophin binding to PTPZ inhibitsits activity (Meng et al., 2000), these results suggest that inhibitionof receptor tyrosine phosphatase activity is a key element underlyingthe neurotrophic or neuroprotective effects of secreted factors such assAPP. We suggest that pharmacological modulation of LAR activity, ormodulation of its interaction with TRIO, or modulation of the TRIOinteraction with KIAA0351 might potentiate the neuroprotective effect ofsAPP.

[0090] As described above and in U.S. patent application Ser. No.09/466,139; International Patent Application No. PCT/US99/30396 (WO00/37483), CIB is a calcium-binding protein that we found to interactwith FKBP25, which is itself a PS1 interactor (see U.S. patentapplication Ser. No. 09/466,139; International Patent Application No.PCT/US99/30396 (WO 00/37483)). Based on its sequence similarity withcalcineurin B, CIB was proposed to be the regulatory subunit of ayet-to-be-discovered calcium-activated phosphatase (Naik et al., 1997).We have suggested that this novel putative phosphatase might control theactivity of the ryanodine receptor, and thus calcium homeostasis (see WeU.S. Patent Application Ser. No. 09/466,139; International PatentApplication No. PCT/US99/30396 (WO 00/37483)). Recently CIB was found toalso interact with PS2 and PS1 (Stabler et al., 1999). Because of thecausal role of PS1 and PS2 mutations in Alzheimer's disease, proteinsthat interact with CIB are likely to play a major role in ADpathogenesis. Using CIB as a bait in a yeast two-hybrid search, we foundthe mixed lineage kinase 2 (MLK2) as a prey.

[0091] MLK2 was originally cloned from human epithelial tumors anddescribed as protein kinases containing two leucine/isoleucine-zipperdomains (Dorow et al., 1993). In another study, MLK2 is called MST anddescribed as a kinase of 953 aa, with an SH3 domain, 2 leucine zipperdomains, and a proline-rich domain (Katoh et al., 1995). Northern blotdata showed that the gene is mostly expressed in brain, skeletal muscle,and testis as a 3.8-kb mRNA. MLK2 belongs to the MAP kinase family andis also called MAP3K10. Interestingly, MLK2-mediated signaling isactivated by polyglutamine-expanded huntingtin, the pathogenic form ofthe protein found in Huntington's disease (Liu et al., 2000). Thus, MLK2appears to mediate neuronal toxicity in some particular condition.Because it interacts with CIB, it is possible that mutations in thepresenilins also activate MLK2, resulting in accelerated neuronalapoptosis, as observed in Alzheimer's. We suggest that pharmacologicalmodulation of MLK2 activity or its interaction with CIB might preventneuronal death.

[0092] BAX is a protein of the Bcl-2 family which mediates apoptosis.Elevated BAX concentrations in the brains of AD patients suggested thatBAX might be responsible for the neuronal death observed in AD (Su etal., 1997). Using BAX as a bait in a yeast two-hybrid search, we foundthe alpha (pore-forming) subunit of the slo (K⁺ activated) potassiumchannel. Potassium channels (K channels) are very diverse in structureand function (Jan and Jan, 1997; Christie, 1995). The slo channel (itsname comes from the fly slowpoke K channel) is a member of the subfamilyof large-conductance calcium activated potassium channels (also calledMaxi K or BK or KCa) which belong to the voltage gated K channel (Kv)family. The BK family contains many splice variants, all of which havethe typical structure of Kv channels: the alpha subunit is ahomotetrameric complex formed by 4 polypeptides, each of which contains6 transmembrane (TM) domains and often large cytosolic N-terminal andC-terminal domains. The channel (pore) region is between TM5 and TM6,while TM4 acts as a voltage sensor, and calcium binding sites are foundin the C-terminal cytosolic domain. Tetraethylammonium (TEA) blocks theactivity of these channels (Jan and Jan, 1997; Christie, 1995). Adysfunction of a large conductance TEA-sensitive K channel wasidentified in fibroblast from AD patients (Etcheberrigaray et al.,1993). Recently, the same channels were found to be activated inresponse to sAPP, resulting in shut down of neuronal activity andprotection against a variety of insults including Ab toxicity (Furukawaet al., 1996a; Goodman and Mattson, 1996). Thus, our finding shows thatBAX, a mediator of apoptosis, interacts with the slo K channel, which isinvolved in the neuroprotective effect of sAPP, and whose activity ifdisrupted in AD fibroblasts. We suggest that pharmacological modulationof the slo K channel activity of modulation of its interaction with BAXmight prevent neuronal apoptosis.

[0093] We reported an interaction between δ-catenin and the focaladhesion kinase 2 (FAK2), also called proline-rich tyrosine kinase 2(PYK2) or cell adhesion kinase β (CAKβ) (see U.S. patent applicationSer. No. 09/466,139; International Patent Application Ser. No.PCT/US99/30396 (WO 00/37483)). Focal adhesion kinases (FAKs) form aspecial subfamily of cytoplasmic protein tyrosine kinases (PTKs). Incontrast to other non-receptor PTKs, FAKs do not contain SH2 or SH3domains, but have a carboxy-terminal proline-rich domain which isimportant for protein-protein interactions (Schaller, 1997; Schaller andParsons, 1994; Parsons et al., 1994). FAK2 is expressed at highestlevels in brain, at medium levels in kidney, lung, and thymus, and atlow levels in spleen and lymphocytes(Avraham et al., 1995). In brain,FAK2 is found at highest levels in the hippocampus and amygdala (Avrahamet al., 1995), two areas severely affected in Alzheimer's disease. FAK2is thought to participate in signal transduction mechanisms elicited bycell-to-cell contacts (Sasaki et al., 1995). It is involved in thecalcium-induced regulation of ion channels, and it is activated by theelevation of intracellular calcium concentration following theactivation of G protein-coupled receptors (GPCRs) that signal though Gαqand the phospholipase C (PLC) pathway (Yu et al., 1996). Thus, FAK2 isan important intermediate signaling molecule between GPCRs activated byneuropeptides or neurotransmitters and downstream signals that modulatethe neuronal activity (channel activation, membrane depolarization).Such a link between intracellular calcium levels, tyrosinephosphorylation, and neuronal activity is clearly important for neuronalsurvival and synaptic plasticity (Siciliano et al., 1996). Theinteraction of FAK2 with δ-catenin and its high levels of expression inhippocampus and amygdala suggest that a disruption of its activity maybe related to neuronal death in AD.

[0094] To gain more insight into the mechanism by which FAK2 mediatesneuronal functions and survival, we used FAK2 as a bait in a yeast twohybrid searches. One of the preys identified was SUR1, the type-1sulfonylurea receptor. Two types of sulfonylurea receptors, SUR1 andSUR2, constitute the regulatory unit of ATP-sensitive inward rectifyingpotassium channels (K_(ATP) channels), while the channel-forming unitbelongs to the Kir6.x family(Bryan and Aguilar-Bryan, 1999; Inagaki andSeino, 1998). A major role of these channels is to link the metabolicstate of the cell to its membrane potential: K_(ATP) channels close uponbinding intracellular ATP to depolarize the cell and open when ATPconcentrations return to resting levels. These channels are involved inevents such as insulin secretion from pancreatic b cells, ischemiaresponses in cardiac and cerebral tissues, and regulation of vascularsmooth muscle tone (Inagaki et al., 1995; Ashcroft and Ashcroft, 1992).The activity of these channels in pancreatic b cells, where they play acrucial role in the secretion of insulin, has been extensively studied:following an elevation of blood glucose levels, the intracellularconcentration of ATP in pancreatic b cells rises, resulting in channelclosure and cell depolarization. This allows Ca²⁺ ions to enter the cellthrough voltage-sensitive Ca²⁺ channels, which will trigger the fusionof insulin secretory vesicles with the plasma membrane and release ofinsulin (Satin, 1996; Ashcroft, 1996). In neurons, the same mechanismsinvolving K_(ATP) channels (linking the metabolic state of the cell toits membrane potential) control neurotransmitter release.

[0095] We also reported an interaction between acetylcholinesterase anda-endosulfine, an endogenous ligand for SUR1 (Virsolvy-Vergine et al.,1992) (see, U.S. patent application Ser. No. 09/466,139; InternationalPatent Application No. PCT/US99/30396 (WO 00/37483)). Because of itsrole in pancreatic beta cells, where is stimulates insulin secretion(Heron et al., 1998), we suggested that in the brain, endosulfinebinding to the sulfonylurea receptor would also shut down K_(ATP)channels, leading to depolarization, Ca²⁺ entry, vesicle fusion, andrelease of the vesicular content into the synaptic cleft. While theactivity of K_(ATP) channels is down-regulated by ATP binding to the SURsubunit, phosphorylation of the Kir6.x subunit by PKA stimulates channelactivity (Lin et al., 2000). Interestingly, endosulfine is also a PKAsubstrate (Virsolvy-Vergine et al., 1992; Heron et al., 1998; Heron etal., 1999). The interaction of SUR1 with FAK2 suggests that additionalphosphorylation events (of any of the channel subunit) might controlchannel activity. K_(ATP) channels are very amenable to pharmacologicalmodulation and drugs that active (K⁺ channels openers (PCO) such asdiazoxide and cromakalim) or inhibit the channels (K⁺ channels blockers(PCB) such as the sulfonylureas glibenclamide and tolbutamide) have beenidentified (Lawson, 1996a; Lawson, 1996b). The function of K_(ATP)channels in the brain is under intense investigation, and the expressionof different K_(ATP) channels in the hippocampus (Zawar et al., 1999)opens a therapeutic opportunity against hippocampal neurodegeneration.In fact, the PCO cromakalim was shown to protect neurons in thehippocampus from glutamate toxicity through a mechanism closely relatedto the control of calcium homeostasis (Lauritzen et al., 1997). Anotherstudy recently showed that K_(ATP) channels are neuroprotective againstthe effects cellular stress caused by energy depletion (Lin et al.,2000). Both calcium homeostasis and energy metabolism are crucialcellular functions that are very affected in neurodegenerative diseasessuch as AD. We suggest that pharmacological modulation of brain Kchannels containing SUR1, or modulation of the interaction between SUR1and FAK2, might help prevent the neuronal loss observed in the brain ofAD patients.

[0096] Cyclic GMP (cGMP) is a small molecule involved in a number ofcellular functions that relate to neuronal survival or death. There isevidence that intracellular cGMP mediates some of the neurotrophiceffects of sAPP (Barger et al., 1995), as well as the neuroprotectiveaction of somatostatin (Forloni et al., 1997). However, there is alsoevidence that intracellular cGMP is neurotoxic while extracellular cGMPis neuroprotective (Montoliu et al., 1999). Recently, Chalimoniuk andStrosznajder looked at the effects of aging and the Ab peptide on nitricoxide (NO) and cGMP signaling in the hippocampus (Chalimoniuk andStrosznajder, 1998). They showed that aging coincided with a decrease inthe basal level of cGMP as a consequence of a more active degradation ofcGMP by a phosphodiesterase in the aged brain as compared to the adultbrain. Moreover, a loss of the NMDA receptor-stimulated enhancement ofthe cGMP level determined in the presence of cGMP-phosphodiesteraseinhibitor 3-isobutyl-1-methylxanthine was observed in hippocampus andcerebellum of aged rats. The neurotoxic Ab25-35 peptide decreasedsignificantly the NMDA receptor-mediated calcium, andcalmodulim-dependent NO synthesis that may then be responsible fordisturbances of the NO and cGMP signaling pathway. They concluded thatcGMP-dependent signal transduction in hippocampus and cerebellum maybecome insufficient in senescent brain and may have functionalconsequences in disturbances of learning and memory processes, and thatthe Ab peptide may be an important factor in decreasing the NO-dependentsignal transduction mediated by NMDA receptors resulting in decreasedcGMP levels. Thus, the effects of cGMP are quite complex and branch intoother pathways such as nitric oxide (NO), NMDA receptor, and calciumhomeostasis. The growing evidence for a neuroprotective effect of cGMP(Barger et al., 1995; Forloni et al., 1997; Chalimoniuk andStrosznajder, 1998) suggests that inhibition of a cGMP-specificphosphodiesterase such as PDE-9A might prove beneficial. Using Mint2 asa bait in a yeast two-hybrid search, we found phosphodiesterase 9A(PDE-9A), a cGMP-specific phosphodiesterase as a prey. The mRNA forPDE-9A was found in all tissues examined, with highest levels in spleen,small intestine, and brain (Fisher et al., 1998). Because PDE-9Ainteracts directly with a protein from the APP pathway (Mint2), andbecause cGMP mediates some of the neurotrophic effects of sAPP (Bargeret al., 1995), we suggest that pharmacological modulation of PDE-9Aactivity or its interaction with Mint2 might potentiates theneurotrophic effects of sAPP and prevent neuronal death observed in ADbrains.

[0097] Using CIB as a bait in a yeast two-hybrid search, we found thestearoyl CoA desaturase (SCD2, also called Delta(9) desaturase) as aprey. This enzyme is a component of the liver microsomal stearoyl-CoAdesaturase system that catalyzes the insertion of a double bond intovarious fatty acyl-CoA substrates. It needs iron as a cofactor and islocalized in the endoplasmic reticulum. In the peripheral nervoussystem, SCD2 is involved in lipid biosynthesis associated withmyelinogenesis (Garbay et al., 1998). Its function in brain is lessclear, as its expression pattern through development does not coincidewell with that of true myelin genes (Garbay et al., 1997). Still, itsfunction in lipid biosynthesis appears to be compatible with a role inmyelination. This interaction between CIB and SCD suggests that themetabolic disorder leading to amyloid plaques and tangles formation,neuronal and synaptic loss, could also downregulate SCD2 activity and inturn result in demyelination, as observed in AD brains. Thus, we proposethat pharmacological modulation of SCD2 or its interaction with CIBmight prevent the myelin loss observed in AD brain and otherneurodegenerative conditions.

[0098] We described the interaction between PS1 and rab 11, a smallGTPase involved in the traffic of intracellular vesicles (see U.S.patent application Ser. No. 09/466,139; International Patent ApplicationNo. PCT/US99/30396 (WO 00/37483)). Rabl 1 is found predominantly inrecycling endosomes (Ullrich et al., 1996; Sheff et al., 1999). It alsoplays a role in the transport of vesicles from the trans-Golgi networkto the plasma membrane and in secretory mechanisms in PC12 cells (Urbeet al., 1993; Chen et al., 1998). These observations confirm the role ofPS1 in vesicular trafficking. We have used rab 11 as a bait in the yeasttwo-hybrid system and found that it interacts with the focal adhesionkinase (FAK). This protein is a tyrosine kinase found at focal adhesionsites, and which mediates the signals elicited by a variety of hormoneand neurotransmitter receptors (Schaller and Parsons, 1994; Parsons etal., 1994; Zachary, 1997; Schlaepfer et al., 1999). These signals areinvolved in the control of a number of cellular events including cellgrowth, migration, and survival. In neurons, FAK is also involved inneurite extension (Park et al., 2000). In addition to its role inneuronal survival and synaptic stability (Girault et al., 1999; Tamuraet al., 1999), FAK activity is known to be disrupted by the Aβ protein(Zhang et al., 1994; Berg et al., 1997). Thus, we have identified atyrosine kinase whose activity is important for neuronal survival andfunction, and which interacts that rab11, a protein involved invesicular trafficking and which binds to PS1. It is thus possible thatFAD mutations in PS1 might alter FAK activity and thus disrupt neuronalfunction and survival.

[0099] To gain more information about the involvement of FAK inneurodegeneration and Alzheimer's disease, we used FAK as a bait in ayeast two-hybrid search and we found casein kinase II (CK2) as a prey.As mentioned above, there is a large body of evidence thatphosphorylation cascades are deeply altered in the brain of AD patients(Jin and Saitoh, 1995; Saitoh et al., 1991; Farlow, 1998). Among thenumerous kinases that are affected in AD, CK2 levels showed a dramaticoverall reduction (84%), although CK2 levels varied a lot between sick(tangle-bearing) neurons and healthy (tangle-free) neurons (limoto etal., 1990). In addition, although CK2 is not part of the paired helicalfilaments (PHF), it is clearly associated with neurofibrillary tangles(Baum et al., 1992). As the CK2 alterations were shown to precede tauaccumulation and tangle formation (Masliah et al., 1992), it wassuggested that CK2 might play a role in tau hyperphosphorylation (andthus tangle formation). However, the biochemical mechanism whereby CK2is activated is still unclear. The observation that CK2 is activated incultured cells treated with insulin, IGF-1, and EGF (Krebs et al., 1988)(factors that signal through tyrosine kinase receptors) suggests thatthe aberrant CK2 cascade observed in AD could reflect an alteredtyrosine phosphorylation balance. Recent studies showed that in turn,CK2 activity can stimulate the tyrosine phosphorylation cascade elicitedby the insulin receptor (Marin et al., 1996), and that CK2 itself canhave tyrosine kinase activity (Marin et al., 1999). Thus, there is clearevidence for a link between CK2 and tyrosine phosphorylation cascades,and the direct interaction between CK2 and FAK suggests that theirrespective activities might be coordinately regulated. We suggest thatadequate pharmacological modulation of FAK activity or CK2 activity, orthe interaction between FAK and rab11 or between FAK and CK2 mightprevent neuronal dysfunction and death observed in the brain ofAlzheimer's patients and other neurodegenerative conditions.

[0100] In the same search, we also identified glutathione-S-transferaseM3 as a FAK interactor, further supporting the involvement of FAK inneurodegeneration and Alzheimer's disease. Free radical neurotoxicity(through the generation of lipid peroxidation products) is welldocumented and was proposed to mediate as least some aspect of Aβtoxicity (Mark et al., 1996; Butterfield, 1997; Whitehouse, 1997),probably through the generation of 4-hydroxynonenal (HNE) (Keller andMattson, 1998). There is also ample evidence that antioxidant moleculesprotect neurons, and in particular, glutathione transferase (GST)protects neurons against toxicity induced by HNE (Xie et al., 1998). Inthis respect, it is interesting that the activity of GST is reduced inAD brain and CSF compared to controls (Lovell et al., 1998). Thus, thisinteraction between FAK and GST generates a new link between twoindependent pathways that are involved in neuron survival and that arealtered in the brains of Alzheimer patients. We suggest that adequatepharmacological modulation of FAK activity or GST activity, or theinteraction between FAK and GST might prevent neuronal dysfunction anddeath observed in the brain of Alzheimer's patients and otherneurodegenerative conditions.

[0101] We reported an interaction between δ-catenin and bcr (break pointcluster), and we explained the relevance of this interaction in thecontext of neurodegeneration and Alzheimer's Disease (see U.S. patentapplication Ser. No. 09/466,139; International Patent Application No.PCT/US99/30396 (WO 00/37483)). In subsequent experiments, we have usedbcr itself has a bait in yeast two-hybrid searches, and have found anumber of interactions, reported here, that strengthen our initial claimthat the bcr protein plays an important role in the brain. Using aC-terminal bait of bcr (aa 1206 to 1271) in a yeast two-hybrid search,we found the neuroendocrine protein Discs Large 3 (NE-dlg, or DLG3),also known as SAP102 (synapse-associated protein 102), and thepostsynaptic density protein PSD95 (DLG4), also known as SAP90. Thesetwo proteins are 67% identical (81% similar) to each other, and bothfunction as synaptic scaffolding proteins that interact with synapticreceptors and associated molecules. PSD95 interacts with the NMDAreceptor (Komau et al., 1995) and this interaction is altered bytransient global ischemia (Takagi et al., 2000). Nitric oxide synthase(NOS), an enzyme that regulates the activity of the NMDA receptor, alsointeracts with PSD95, and this interaction is displaced by CAPON(Jaffrey et al., 1998). DLG3 also interacts with the NMDA receptor (Lauet al., 1996; Muller et al., 1996). The well documented role of the NMDAreceptor in long-term potentiation (LTP) in the hippocampus (Muller etal., 1995; Sans et al., 2000) suggests that proteins such as PSD95 andDLG3 play important synaptic functions underlying learning and memory.In addition, PSD95 also interacts with several types of potassiumchannels (Laube et al., 1996; Nehring et al., 2000). The activity ofthose channels is clearly involved in neuronal survival (Holm et al.,1997; Mattson, 1997a), particularly in the hippocampus (Zawar andNeumcke, 2000). Thus, through it clustering function of potassiumchannels, PSD95 also plays a role in neuronal survival.

[0102] It is also interesting to note that PSD95 interacts with SynGAP(Kim et al., 1998), an activating protein for the GTPase Ras. Thus,PSD95 interacts with at least two proteins that activate GTPases: SynGAPand bcr (Braselmann and McCormick, 1995; Diekmann et al., 1995). Usingthe same C-terminal bait of bcr (aa 1206 to 1271) in a yeast two-hybridsearch, we also found the transcription factor HTF4A as an interactor.HTF4A is a protein of 682 amino acids, from the myc family of basichelix-loop-helix (bHLH) transcription factors. HTF4A activates thetranscription of a number of genes by binding to E-box motifs, includingthe gene for the α1 acetylcholine receptor (AChR) (Neville et al.,1998). HTF4A also stimulates the transcription of the vgf gene (Di Roccoet al., 1997), a secreted neuropeptide whose expression is induced byseveral neurotrophins (Snyder et al., 1998). Decreased levels of vgfmRNA in the hippocampus have been correlated with age-induced cognitivedecline in rats (Sugaya et al., 1998). Thus, reduced HTF4A-dependenttranscriptional activity in the hippocampus could be associated withage-related memory loss. This interaction strengthens the finding thatbcr and associated proteins play an important synaptic function in thehippocampus.

[0103] Using a bcr bait from aa 856 to 1226 in a yeast two-hybridsearch, we found a novel human protein as an interactor. This novelprotein is 94% identical to mouse semaphorin F (M-sema F). Thesemaphorins belong to a family of secreted and membrane bound proteinsinvolved in the nervous system development and axonal guidance.Semaphorin F is a transmembrane form (Inagaki et al., 1995). Recently,the cytosolic C-terminal domain of M-sema F was found to interact withGIPC (also named Semcapl) (Wang et al., 1999). Thus, semaphorin F is acommon interactor to bcr and GIPC, as is δ-catenin. Using a C-terminalbait of bcr (aa 1206 to 1271) in a yeast two-hybrid search, we alsofound SRCAP (Snf2-related CBP activator protein) as an interactor. Thisfinding further support the involvement of bcr in hippocampal synapticfunction. CBP (CREB-binding protein) is a co-activator for a number oftranscription factors and interacts with a number of proteins such ashistone acetyltransferases, general transcription factors, and otherco-activators.

[0104] Recently, a novel CBP-interacting protein was identified andnamed SRCAP (Johnston et al., 1999). This protein has ATPase activityand activates transcription of several genes. Because bcr interacts withproteins such as δ-catenin, PSD95, Semaphorin F, and DLG3 (all involvedin synaptic function), and because CREB-mediated immediate earlytranscription is essential for LTP in the hippocampus (Walton et al.,1999), this interaction between bcr and SRCAP brings together theessential components of hippocampal synaptic modulation. Because bcr wasfound as an interactor with δ-catenin (see U.S. patent application Ser.No. 09/466,139; International Patent Application No. PCT/US99/30396 (WO00/37483)), the interactions reported in the present application (bcrwith PSD95, DLG3, Semaphorin F, HTF4A, and SRCAP) generate a pathwaythat links δ-catenin and to synaptic functions and neuronal survival. Wesuggest that adequate pharmacological modulation the interactionsbetween bcr and any of the five bcr interactors described here mightprevent synaptic dysfunction and neuronal death observed in the brain ofAlzheimer's patients and other neurodegenerative conditions.

[0105] We report interactions between PSD95 and the novel proteinPN7740. PSD95 is a member of the MAGUK family (membrane associatedguanylate kinase) and contains three PDZ domains, one SH3 domain, andone guanylate kinase (GK) domain (Wheal et al., 1998; Dimitratos et al.,1999). Also called DLG4 and SAP-90 (Kistner et al., 1993; Stathakis etal., 1997), PSD95 is found at the post-synaptic density where itinteracts with other synaptic scaffolding proteins and with synapticsignalling proteins such as neurotransmitter receptors and channels(e.g. NMDA receptors, potassium channels) (Komau et al., 1995; Nagano etal., 1998; Lau et al., 1996; Nehring et al., 2000). PN7740 is a novelprotein that we reported as an Fe65 interactor (see above). Thefull-length cDNA for PN7740 contains a open reading frame (ORF) codingfor 372 amino acids. The putative ATG initiation codon is preceded by apurine (G) residue in position -3, and by several upstream STOP codons,suggesting that it represents the authentic initiation codon. At the endof the 3′ UTR (untranslated region), we found a canonicalpolyadenylation signal (AATAAA) shortly before the poly A itself. Aphosphatase 2C domain was found from amino acids 104 to 339. Thus, weidentified a novel phosphatase that binds to the first PTB domain ofFe65.

[0106] The proteins disclosed in the present invention were found tointeract with PS1, APP or other proteins involved in AD, in the yeasttwo-hybrid system. Because of the involvement of these proteins in AD,the proteins disclosed herein also participate in the pathogenesis ofAD. Therefore, the present invention provides a list of uses of thoseproteins and DNA encoding those proteins for the development ofdiagnostic and therapeutic tools against AD. This list includes, but isnot limited to, the following examples.

Two-Hybrid System

[0107] The principles and methods of the yeast two-hybrid system havebeen described in detail elsewhere (e.g., Bartel and Fields, 1997;Bartel et al., 1993; Fields and Song, 1989; Chevray and Nathans, 1992).The following is a description of the use of this system to identifyproteins that interact with a protein of interest, such as PS1.

[0108] The target protein is expressed in yeast as a fusion to theDNA-binding domain of the yeast Gal4p. DNA encoding the target proteinor a fragment of this protein is amplified from cDNA by PCR or preparedfrom an available clone. The resulting DNA fragment is cloned byligation or recombination into a DNA-binding domain vector (e.g., pGBT9,pGBT.C, pAS2-1) such that an in-frame fusion between the Gal4p andtarget protein sequences is created.

[0109] The target gene construct is introduced, by transformation, intoa haploid yeast strain. A library of activation domain fusions (i.e.,adult brain cDNA cloned into an activation domain vector) is introduced,by transformation into a haploid yeast strain of the opposite matingtype. The yeast strain that carries the activation domain constructscontains one or more Gal4p-responsive reporter gene(s), whose expressioncan be monitored. Examples of some yeast reporter strains include Y190,PJ69, and CBY14a. An aliquot of yeast carrying the target gene constructis combined with an aliquot of yeast carrying the activation domainlibrary. The two yeast strains mate to form diploid yeast and are platedon media that selects for expression of one or more Gal4p-responsivereporter genes. Colonies that arise after incubation are selected forfurther characterization.

[0110] The activation domain plasmid is isolated from each colonyobtained in the two-hybrid search. The sequence of the insert in thisconstruct is obtained by the dideoxy nucleotide chain terminationmethod. Sequence information is used to identify the gene/proteinencoded by the activation domain insert via analysis of the publicnucleotide and protein databases. Interaction of the activation domainfusion with the target protein is confirmed by testing for thespecificity of the interaction. The activation domain construct isco-transformed into a yeast reporter strain with either the originaltarget protein construct or a variety of other DNA-binding domainconstructs. Expression of the reporter genes in the presence of thetarget protein but not with other test proteins indicates that theinteraction is genuine.

[0111] In addition to the yeast two-hybrid system, other geneticmethodologies are available for the discovery or detection ofprotein-protein interactions. For example, a mammalian two-hybrid systemis available commercially (Clontech, Inc.) that operates on the sameprinciple as the yeast two-hybrid system. Instead of transforming ayeast reporter strain, plasmids encoding DNA-binding and activationdomain fusions are transfected along with an appropriate reporter gene(e.g., lacZ) into a mammalian tissue culture cell line. Becausetranscription factors such as the Saccharomyces cerevisiae Gal4p arefunctional in a variety of different eukaryotic cell types, it would beexpected that a two-hybrid assay could be performed in virtually anycell line of eukaryotic origin (e.g., insect cells (SF9), fungal cells,worm cells, etc.). Other genetic systems for the detection ofprotein-protein interactions include the so-called SOS recruitmentsystem (Aronheim et al., 1997).

Protein-protein Interactions

[0112] Protein interactions are detected in various systems includingthe yeast two-hybrid system, affinity chromatography,co-immunoprecipitation, subcellular fractionation and isolation of largemolecular complexes. Each of these method is well characterized and canbe readily performed by one skilled in the art. See, e.g., U.S. Pat.Nos. 5,622,852 and 5,773,218, and PCT published application Nos. WO97/27296 and WO 99/65939, each of which are incorporated herein byreference.

[0113] The protein of interest can be produced in eukaryotic orprokaryotic systems. A cDNA encoding the desired protein is introducedin an appropriate expression vector and transfected in a host cell(which could be bacteria, yeast cells, insect cells, or mammaliancells). Purification of the expressed protein is achieved byconventional biochemical and immunochemical methods well known to thoseskilled in the art. The purified protein is then used for affinitychromatography studies: it is immobilized on a matrix and loaded on acolumn. Extracts from cultured cells or homogenized tissue samples arethen loaded on the column in appropriate buffer, and non-bindingproteins are eluted. After extensive washing, binding proteins orprotein complexes are eluted using various methods such as a gradient ofpH or a gradient of salt concentration. Eluted proteins can then beseparated by two-dimensional gel electrophoresis, eluted from the gel,and identified by micro-sequencing. The purified proteins can also beused for affinity chromatography to purify interacting proteinsdisclosed herein. All of these methods are well known to those skilledin the art.

[0114] Similarly, both proteins of the complex of interest (orinteracting domains thereof) can be produced in eukaryotic orprokaryotic systems. The proteins (or interacting domains) can be undercontrol of separate promoters or can be produced as a fusion protein.The fusion protein may include a peptide linker between the proteins (orinteracting domains) which, in one embodiment, serves to promote theinteraction of the proteins (or interacting domains). All of thesemethods are also well known to those skilled in the art.

[0115] Purified proteins of interest, individually or a complex, canalso be used to generate antibodies in rabbit, mouse, rat, chicken,goat, sheep, pig, guinea pig, bovine, and horse. The methods used forantibody generation and characterization are well known to those skilledin the art. Monoclonal antibodies are also generated by conventionaltechniques. Single chain antibodies are further produced by conventionaltechniques.

[0116] DNA molecules encoding proteins of interest can be inserted inthe appropriate expression vector and used for transfection ofeukaryotic cells such as bacteria, yeast, insect cells, or mammaliancells, following methods well known to those skilled in the art.Transfected cells expressing both proteins of interest are then lysed inappropriate conditions, one of the two proteins is immunoprecipitatedusing a specific antibody, and analyzed by polyacrylamide gelelectrophoresis. The presence of the binding protein(co-immunoprecipitated) is detected by immunoblotting using an antibodydirected against the other protein. Co-immunoprecipitation is a methodwell known to those skilled in the art.

[0117] Transfected eukaryotic cells or biological tissue samples can behomogenized and fractionated in appropriate conditions that willseparate the different cellular components. Typically, cell lysates arerun on sucrose gradients, or other materials that will separate cellularcomponents based on size and density. Subcellular fractions are analyzedfor the presence of proteins of interest with appropriate antibodies,using immunoblotting or immunoprecipitation methods. These methods areall well known to those skilled in the art.

Disruption of Protein-protein Interactions

[0118] It is conceivable that agents that disrupt protein-proteininteractions can be beneficial in AD. Each of the methods describedabove for the detection of a positive protein-protein interaction canalso be used to identify drugs that will disrupt said interaction. As anexample, cells transfected with DNAs coding for proteins of interest canbe treated with various drugs, and co-immunoprecipitations can beperformed. Alternatively, a derivative of the yeast two-hybrid system,called the reverse yeast two-hybrid system (Lenna and Hannink, 1996),can be used, provided that the two proteins interact in the straightyeast two-hybrid system.

Modulation of Protein-protein Interactions

[0119] Since the interactions described herein are involved in the ADpathway, the identification of agents which are capable of modulatingthe interactions will provide agents which can be used to track AD or touse lead compounds for development of therapeutic agents. An agent maymodulate expression of the genes of interacting proteins, thus affectinginteraction of the proteins. Alternatively, the agent may modulate theinteraction of the proteins. The agent may modulate the interaction ofwild-type with wild-type proteins, wild-type with mutant proteins, ormutant with mutant proteins. Agents which may be used to modulate theprotein interaction include a peptide, an antibody, a nucleic acid, anantisense compound or a ribozyme. The nucleic acid may encode theantibody or the antisense compound. The peptide may be at least 4 aminoacids of the sequence of either of the interacting proteins.Alternatively, the peptide may be from 4 to 30 amino acids (or from 8 to20 amino acids) that is at least 75% identical to a contiguous span ofamino acids of either of the interacting proteins. The peptide may becovalently linked to a transporter capable of increasing cellular uptakeof the peptide. Examples of a suitable transporter include penetrating,l-Tat₄₉₋₅₇, d-Tat_(49═57), retro-inverso isomers of l- or d-Tat₄₉₋₅₇,L-arginine oligomers, D- arginine oligomers, L-lysine oligomers,D-lysine oligomers, L-histine oligomers, D-histine oligomers,L-ornithine oligomers, D-ornithine oligomers, short peptide sequencesderived from fibroblast growth factor, Galparan, and HSV-1 structuralprotein VP22, and peptoid analogs thereof. Agents can be tested usingtransfected host cells, cell lines, cell models or animals, such asdescribed herein, by techniques well known to those of ordinary skill inthe art, such as disclosed in U.S. Pat. Nos. 5,622,852 and 5,773,218,and PCT published application Nos. WO 97/27296 and WO 99/65939, each ofwhich are incorporated herein by reference. The modulating effect of theagent can be tested in vivo or in vitro. Agents can be provided fortesting in a phage display library or a combinatorial library. Exemplaryof a method to screen agents is to measure the effect that the agent hason the formation of the protein complex.

Mutation Screening

[0120] The proteins disclosed in the present invention interact with oneor more proteins known to be involved in AD. Mutations in interactingproteins could also be involved in the development of AD, for example,through a modification of protein-protein interaction, or a modificationof enzymatic activity, modification of receptor activity, or through anunknown mechanism. Therefore, mutations can be found by sequencing thegenes for the proteins of interest in patients having the physiologicaldisorder, such as insulin, and non-affected controls. A mutation inthese genes, especially in that portion of the gene involved in proteininteractions in the physiological pathway, can be used as a diagnostictool and the mechanistic understanding the mutation provides can helpdevelop a therapeutic tool.

Screening for at-risk Individuals

[0121] Individuals can be screened to identify those at risk byscreening for mutations in the protein disclosed herein and identifiedas described above. Alternatively, individuals can be screened byanalyzing the ability of the proteins of said individual disclosedherein to form natural complexes. Further, individuals can be screenedby analyzing the levels of the complexes or individual proteins of thecomplexes or the mRNA encoding the protein members of the complexes.Techniques to detect the formation of complexes, including thosedescribed above, are known to those skilled in the art. Techniques andmethods to detect mutations are well known to those skilled in the art.Techniques to detect the level of the complexes, proteins or mRNA arewell known to those skilled in the art.

Cellular Models of AD

[0122] A number of cellular models of AD have been generated and the useof these models is familiar to those skilled in the art. As an example,secretion of the Aβ peptide from cultured cells can be measured withappropriate antibodies. Likewise, the proportion of Aβ40 and Aβ42 can bereadily determined. Neuron survival assays and neurite extension assaysin the presence of various toxic agents (the Aβ peptide, free radicals,others) are also well known to those skilled in the art. Primaryneuronal cultures or established neuronal cell lines can be transfectedwith expression vectors encoding the proteins of interest, eitherwild-type proteins or Alzheimer's-associated mutant proteins. The effectof these proteins on parameters relevant to AD (Aβ secretion, neuronalsurvival, neurite extension, or others) can be readily measured.Furthermore, these cellular systems can be used to screen drugs thatwill influence those parameters, and thus be potential therapeutic toolsin AD. Alternatively, instead of transfecting the DNA encoding theprotein of interest, the purified protein of interest can be added tothe culture medium of the neurons, and the relevant parameters measured.

Animal Models

[0123] The DNA encoding the protein of interest can be used to createanimals that overexpress said protein, with wild-type or mutantsequences (such animals are referred to as “transgenic”), or animalswhich do not express the native gene but express the gene of a secondanimal (referred to as “transplacement”), or animals that do not expresssaid protein (referred to as “knock-out”). The knock-out animal may bean animal in which the gene is knocked out at a determined time. Thegeneration of transgenic, transplacement and knock-out animals (normaland conditioned) uses methods well known to those skilled in the art.

[0124] In these animals, parameters relevant to AD can be measured.These include Aβ secretion in the cerebrospinal fluid, Aβ secretion fromprimary cultured cells, the neurite extension activity and survival rateof primary cultured cells, concentration of Aβ peptide in homogenatesfrom various brain regions, the presence of neurofibrillary tangles andsenile plaques in the brain, the total amyloid load in the brain, thedensity of synaptic terminals and the neuron counts in the brain.Additionally, behavioral analysis can be performed to measure learningand memory performance of the animals. The tests include, but are notlimited to, the Morris water maze and the radial-arm maze. Themeasurements of biochemical and neuropathological parameters, and ofbehavioral parameters (learning and memory), are performed using methodswell known to those skilled in the art. These transgenic, transplacementand knock-out animals can also be used to screen drugs that mayinfluence these biochemical, neuropathological, and behavioralparameters relevant to AD. Cell lines can also be derived from theseanimals for use as cellular models of AD, or in drug screening.

Rational Drug Design

[0125] The goal of rational drug design is to produce structural analogsof biologically active polypeptides of interest or of small moleculeswith which they interact (e.g., agonists, antagonists, inhibitors) inorder to fashion drugs which are, for example, more active or stableforms of the polypeptide, or which, e.g., enhance or interfere with thefunction of a polypeptide in vivo. Several approaches for use inrational drug design include analysis of three-dimensional structure,alanine scans, molecular modeling and use of anti-id antibodies. Thesetechniques are well known to those skilled in the art. Such techniquesmay include providing atomic coordinates defining a three-dimensionalstructure of a protein complex formed by said first polypeptide and saidsecond polypeptide, and designing or selecting compounds capable ofinterfering with the interaction between a first polypeptide and asecond polypeptide based on said atomic coordinates.

[0126] Following identification of a substance which modulates oraffects polypeptide activity, the substance may be further investigated.Furthermore, it may be manufactured and/or used in preparation, i.e.,manufacture or formulation, or a composition such as a medicament,pharmaceutical composition or drug. These may be administered toindividuals.

[0127] A substance identified as a modulator of polypeptide function maybe peptide or non-peptide in nature. Non-peptide “small molecules” areoften preferred for many in vivo pharmaceutical uses. Accordingly, amimetic or mimic of the substance (particularly if a peptide) may bedesigned for pharmaceutical use.

[0128] The designing of mimetics to a known pharmaceutically activecompound is a known approach to the development of pharmaceuticals basedon a “lead” compound. This approach might be desirable where the activecompound is difficult or expensive to synthesize or where it isunsuitable for a particular method of administration, e.g., purepeptides are unsuitable active agents for oral compositions as they tendto be quickly degraded by proteases in the alimentary canal. Mimeticdesign, synthesis and testing is generally used to avoid randomlyscreening large numbers of molecules for a target property.

[0129] Once the pharmacophore has been found, its structure is modeledaccording to its physical properties, e.g., stereochemistry, bonding,size and/or charge, using data from a range of sources, e.g.,spectroscopic techniques, x-ray diffraction data and NMR. Computationalanalysis, similarity mapping (which models the charge and/or volume of apharmacophore, rather than the bonding between atoms) and othertechniques can be used in this modeling process.

[0130] A template molecule is then selected, onto which chemical groupsthat mimic the pharmacophore can be grafted. The template molecule andthe chemical groups grafted thereon can be conveniently selected so thatthe mimetic is easy to synthesize, is likely to be pharmacologicallyacceptable, and does not degrade in vivo, while retaining the biologicalactivity of the lead compound. Alternatively, where the mimetic ispeptide-based, further stability can be achieved by cyclizing thepeptide, increasing its rigidity. The mimetic or mimetics found by thisapproach can then be screened to see whether they have the targetproperty, or to what extent it is exhibited. Further optimization ormodification can then be carried out to arrive at one or more finalmimetics for in vivo or clinical testing.

Diagnostic Assays

[0131] The identification of the interactions disclosed herein enablesthe development of diagnostic assays and kits, which can be used todetermine a predisposition to or the existence of a physiologicaldisorder. In one aspect, one of the proteins of the interaction is usedto detect the presence of a “normal” second protein (i.e., normal withrespect to its ability to interact with the first protein) in a cellextract or a biological fluid, and further, if desired, to detect thequantitative level of the second protein in the extract or biologicalfluid. The absence of the “normal” second protein would be indicative ofa predisposition or existence of the physiological disorder. In a secondaspect, an antibody against the protein complex is used to detect thepresence and/or quantitative level of the protein complex. The absenceof the protein complex would be indicative of a predisposition orexistence of the physiological disorder.

Nucleic Acids and Proteins

[0132] A nucleic acid or fragment thereof has substantial identity withanother if, when optimally aligned (with appropriate nucleotideinsertions or deletions) with the other nucleic acid (or itscomplementary strand), there is nucleotide sequence identity in at leastabout 60% of the nucleotide bases, usually at least about 70%, moreusually at least about 80%, preferably at least about 90%, morepreferably at least about 95% of the nucleotide bases, and morepreferably at least about 98% of the nucleotide bases. A protein orfragment thereof has substantial identity with another if, optimallyaligned, there is an amino acid sequence identity of at least about 30%identity with an entire naturally-occurring protein or a portionthereof, usually at least about 70% identity, more usually at leastabout 80% identity, preferably at least about 90% identity, morepreferably at least about 95% identity, and most preferably at leastabout 98% identity.

[0133] Identity means the degree of sequence relatedness between twopolypeptide or two polynucleotides sequences as determined by theidentity of the match between two strings of such sequences. Identitycan be readily calculated. While there exist a number of methods tomeasure identity between two polynucleotide or polypeptide sequences,the term “identity” is well known to skilled artisans (ComputationalMolecular Biology, Lesk, A. M., ed., Oxford University Press, New York,1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed.,Academic Press, New York, 1993; Computer Analysis of Sequence Data, PartI, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey,1994; Sequence Analysis in Molecular Biology, von Heinje, G., AcademicPress, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux,J., eds., M Stockton Press, New York, 1991). Methods commonly employedto determine identity between two sequences include, but are not limitedto those disclosed in Guide to Huge Computers, Martin J. Bishop, ed.,Academic Press, San Diego, 1994, and Carillo, H., and Lipman, D., SIAM JApplied Math. 48:1073 (1988). Preferred methods to determine identityare designed to give the largest match between the two sequences tested.Such methods are codified in computer programs. Preferred computerprogram methods to determine identity between two sequences include, butare not limited to, GCG (Genetics Computer Group, Madison Wis.) programpackage (Devereux, J., et al., Nucleic Acids Research 12(1).387 (1984)),BLASTP, BLASTN, FASTA (Altschul et al. (1990); Altschul et al. (1997)).The well-known Smith Waterman algorithm may also be used to determineidentity.

[0134] Alternatively, substantial homology or similarity exists when anucleic acid or fragment thereof will hybridize to another nucleic acid(or a complementary strand thereof) under selective hybridizationconditions, to a strand, or to its complement. Selectivity ofhybridization exists when hybridization which is substantially moreselective than total lack of specificity occurs. Nucleic acidhybridization will be affected by such conditions as salt concentration,temperature, or organic solvents, in addition to the base composition,length of the complementary strands, and the number of nucleotide basemismatches between the hybridizing nucleic acids, as will be readilyappreciated by those skilled in the art. Stringent temperatureconditions will generally include temperatures in excess of 30° C.,typically in excess of 37° C., and preferably in excess of 45° C.Stringent salt conditions will ordinarily be less than 1000 mM,typically less than 500 mM, and preferably less than 200 mM. However,the combination of parameters is much more important than the measure ofany single parameter. See, e.g., Asubel, 1992; Wetmur and Davidson,1968.

[0135] The terms “isolated”, “substantially pure”, and “substantiallyhomogeneous” are used interchangeably to describe a protein orpolypeptide which has been separated from components which accompany itin its natural state. A monomeric protein is substantially pure when atleast about 60 to 75% of a sample exhibits a single polypeptidesequence. A substantially pure protein will typically comprise about 60to 90% W/W of a protein sample, more usually about 95%, and preferablywill be over about 99% pure. Protein purity or homogeneity may beindicated by a number of means well known in the art, such aspolyacrylamide gel electrophoresis of a protein sample, followed byvisualizing a single polypeptide band upon staining the gel. For certainpurposes, higher resolution may be provided by using HPLC or other meanswell known in the art which are utilized for purification.

[0136] Large amounts of the nucleic acids of the present invention maybe produced by (a) replication in a suitable host or transgenic animalsor (b) chemical synthesis using techniques well known in the art.Constructs prepared for introduction into a prokaryotic or eukaryotichost may comprise a replication system recognized by the host, includingthe intended polynucleotide fragment encoding the desired polypeptide,and will preferably also include transcription and translationalinitiation regulatory sequences operably linked to the polypeptideencoding segment. Expression vectors may include, for example, an originof replication or autonomously replicating sequence (ARS) and expressioncontrol sequences, a promoter, an enhancer and necessary processinginformation sites, such as ribosome-binding sites, RNA splice sites,polyadenylation sites, transcriptional terminator sequences, and mRNAstabilizing sequences. Secretion signals may also be included whereappropriate which allow the protein to cross and/or lodge in cellmembranes, and thus attain its functional topology, or be secreted fromthe cell. Such vectors may be prepared by means of standard recombinanttechniques well known in the.

[0137] The nucleic acid or protein may also be incorporated on amicroarray. The preparation and use of microarrays are well known in theart. Generally, the microarray may contain the entire nucleic acid orprotein, or it may contain one or more fragments of the nucleic acid orprotein. Suitable nucleic acid fragments may include at least 17nucleotides, at least 21 nucleotides, at least 30 nucleotides or atleast 50 nucleotides of the nucleic acid sequence, particularly thecoding sequence. Suitable protein fragments may include at least 4 aminoacids, at least 8 amino acids, at least 12 amino acids, at least 15amino acids, at least 17 amino acids or at least 20 amino acids. Thus,the present invention is also directed to such nucleic acid and proteinfragments.

EXAMPLES

[0138] The present invention is further detailed in the followingExamples, which are offered by way of illustration and are not intendedto limit the invention in any manner. Standard techniques well known inthe art or the techniques specifically described below are utilized.

Example 1 Yeast Two-Hybrid System

[0139] The principles and methods of the yeast two-hybrid systems havebeen described in detail (Bartel and Fields, 1997). The following isthus a description of the particular procedure that was used, which wasapplied to all proteins.

[0140] The cDNA encoding the bait protein was generated by PCR frombrain cDNA. Gene-specific primers were synthesized with appropriatetails added at their 5′ ends to allow recombination into the vectorpGBTQ. The tail for the forward primer was5′-GCAGGAAACAGCTATGACCATACAGTCAGCGGCCGCCACC-3′ (SEQ ID NO: 1) and thetail for the reverse primer was5′-ACGGCCAGTCGCGTGGAGTGTTATGTCATGCGGCCGCTA-3′ (SEQ ID NO:2). The tailedPCR product was then introduced by recombination into the yeastexpression vector pGBTQ, which is a close derivative of pGBTC (Bartel etal., 1996) in which the polylinker site has been modified to include M13sequencing sites. The new construct was selected directly in the yeastJ693 for its ability to drive tryptophane synthesis (genotype of thisstrain: Mat α, ade2, his3, leu2, trp1, URA3::GAL1-lacZ LYS2::GAL1-HIS3gal4del gal8Odel cyhR2). In these yeast cells, the bait is produced as aC-terminal fusion protein with the DNA binding domain of thetranscription factor Gal4 (amino acids 1 to 147). A total human brain(37 year-old male Caucasian) cDNA library cloned into the yeastexpression vector pACT2 was purchased from Clontech (human brainMATCHMAKER cDNA, cat. #HL4004AH), transformed into the yeast strain J692(genotype of this strain: Mat α, ade2, his3, leu2, trp1, URA3::GAL1-lacZLYS2::GAL1-HIS3 gal4del gal80del cyhR2), and selected for the ability todrive leucine synthesis. In these yeast cells, each cDNA is expressed asa fusion protein with the transcription activation domain of thetranscription factor Gal4 (amino acids 768 to 881) and a 9 amino acidhemagglutinin epitope tag. J693 cells (Mat α type) expressing the baitwere then mated with J692 cells (Mat α type) expressing proteins fromthe brain library. The resulting diploid yeast cells expressing proteinsinteracting with the bait protein were selected for the ability tosynthesize tryptophane, leucine, histidine, and β-galactosidase. DNA wasprepared from each clone, transformed by electroporation into E. colistrain KC8 (Clontech KC8 electrocompetent cells, cat #C2023-1), and thecells were selected on ampicillin-containing plates in the absence ofeither tryptophane (selection for the bait plasmid) or leucine(selection for the brain library plasmid). DNA for both plasmids wasprepared and sequenced by di-deoxynucleotide chain termination method.The identity of the bait cDNA insert was confirmed and the cDNA insertfrom the brain library plasmid was identified using BLAST programagainst public nucleotides and protein databases. Plasmids from thebrain library (preys) were then individually transformed into yeastcells together with a plasmid driving the synthesis of lamin fused tothe Gal4 DNA binding domain. Clones that gave a positive signal afterβ-galactosidase assay were considered false-positives and discarded.Plasmids for the remaining clones were transformed into yeast cellstogether with plasmid for the original bait. Clones that gave a positivesignal after β-galactosidase assay were considered true positives.

Examples 2-33 Identification of Protein-Protein Interactions

[0141] A yeast two-hybrid system as described in Example 1 using aminoacids of the bait as set forth in Table 36 was performed. The clone thatwas identified by this procedure for each bait is set forth in Table 36as the prey. The “aa” refers to the amino acids of the bait or prey. TheGenBank and Sw-Pr columns refer to the GenBank and Swiss Proteinaccession numbers, respectively.

[0142] One novel protein, identified as PN7740, was discovered in theseExamples. The cDNA sequence and protein sequence for PN7740 are setforth in Tables 34 and 35, respectively. TABLE 34 cDNA Sequence ofPN7740 (SEQ ID NO:3)CGAGAATTTCCAGCAGGCAAGGCAGTGGCCGCTTTGACTGCTTGCTTCGGAGATCCGAGACGACGGAGAAGGCACTCTTATTTACCGACCAAGAAAGCTCCTCCCCCGTCCTCCGTTAGCTAATTAAAACATTTTTCAGGGACGTAGCCATCCAGAGACATTCCATTATTGTTCCATTGACCTTTCCCTCATCACTGAGTCCTTTGGAGCTGAGTT ATG TCAACAGCTGCCTTAATTACTTTGGTCAGAAGTGGTGGGAACCAGGTGAGAAGGAGAGTGCTGCTAAGCTCCCGCCTGCTGCAGGACGACAGGCGGGTGACACCCACGTGCCACAGCTCCACTTCAGAGCCTAGGTGTTCTCGGTTTGACCCAGATGGTAGTGGGAGTCCAGCTACCTGGGACAATTTTGGGATCTGGGATAACCGCATTGATGAGCCAATTCTGCTGCCACCCAGCATTAAGTATGGCAAGCCAATTCCCAAAATCAGCTTGGAAAATGTGGGGTGCGCCTCACAGATTGGCAAACGGAAAGAGAATGAAGATCGGTTTGACTTCGCTCAGCTGACAGATGAGGTCCTGTACTTTGCAGTGTATGATGGACACGGTGGACCTGCAGCAGCTGATTTCTGTCATACCCACATGGAGAAATGTATTATGGATTTGCTTCCTAAGGAGAAGAACTTGGAAACTCTGTTGACCTTGGCTTTTCTAGAAATAGATAAAGCCTTTTCGAGTCATGCCCGCCTGTCTGCTGATGCAACTCTTCTGACCTCTGGGACTACTGCAACAGTAGCCCTATTGCGAGATGGTATTGAACTGGTTGTAGCCAGTGTTGGGGACAGCCGGGCTATTTTGTGTAGAAAAGGAAAACCCATGAAGCTGACCATTGACCATACTCCAGAAAGAAAAGATGAAAAAGAAAGGATCAAGAAATGTGGTGGTTTTGTAGCTTGGAATAGTTTGGGGCAGCCTCACGTAAATGGCAGGCTTGCAATGACAAGAAGTATTGGAGATTTGGACCTTAAGACCAGTGGTGTCATAGCAGAACCTGAAACTAAGAGGATTAAGTTACATCATGCTGATGACAGCTTCCTGGTCCTCACCACAGATGGAATTAACTTCATGGTGAATAGTCAAGAGATTTGTGACTTTGTCAATCAGTGCCATGATCCCAACGAAGCAGCCCATGCGGTGACTGAACAGGCAATACAGTACGGTACTGAGGATAACAGTACTGCAGTAGTAGTGCCTTTTGGTGCCTGGGGAAAATATAAGAACTCTGAAATCAACTTCTCATTCAGCAGAAGCTTTGCCTCCAGTGGACGATGGGCC TGA TTACCAGCTGGGACTTAGAGTTTCTGTGCAACAGTTTTTCACTGAGCATGTCAAGAAACTGATAAGATCAAAAAGGTCTCCTAACTCACTAGATCAGCGCACAAGTCAGTGTAAACCACTTAGATAGTAGTTTTTTCATAAATGCTCATCATATTTATGTTCCGCTGTACATGTTCAGTATAAATATATGTGTAGTGAAGCTACTGTGAGTCTTTAAATGGAAAGAGCAAATGAGAAGTGGTTTGGATACACTTGATGAGAGATGAGAGTGTCACATTAATAATTTTTAAGACTCTTAGGCAGCTATGGGTTTCTTTTGATCATTTTTGTTCTTTATTCATTTGAACACGTTTTTGAAGTTCTTCAAAACTAGTCAGTTTGAATTTTGACAGCTATTCAATATGTGATCTCCAAGTTTAAAAAAATTTTTTTCCAGACTTCCCTAATCCTAAAATGCGAGTTTTTATTTTTAATAACTGTACCAAGGAATAAGTATGAAAACAGTTCTCTGTTACCATATTTTGTATTCTGGACCACTTACTGGTGAAAGCAACCATGCAAAAGAAATTAATTTGGCCAGGCACAGTGGCTCATGCCTGTAATCCCAAATTGCTGGGATTACAGCACTGTGCCCTCCTAGGAAATTATTTTTTAAGTGAAATTTTATTTTTATTTTTTTTAGGATTTTGGTAGAGAATGAGTAGGCCTACTCATCAATATCAAACAGGACATTTAGTTTCTTTCCTTAGAACAGACATAAATTTAATTTCATGGTAATATGATAATAAGAAAATGCTTCTATTTTTCTTTAGCACCTCCATGGTTCTCATATACCCATGTCTGTAAAAAGTGACATGAGAATTTTGTTGGGTTACATTTTATTGTATTTATTAGATTCGCTTATATAGATGACTTAGGCAGAAATAAAGTCATGTCTTTAGAAGGTGAACAAGCCAACTTGTGATGGCCTGCCTTTTGCTTTTGGCAGTTGGGATGAGAACAATTGACTCTCCCATTGGTTGTTAGATAGTTGAAATGGTGCGTTGGTGGTCATACTTAGTGTTCTAGGCTGTGAAATCATGGAGTTCTTCCACTTCCAAGAATGACTCATTTGCTGTTGGATTCTAGTACAGAATTTAGCAGCCTGATGTGTCCCCAAACTGATTTAATTTCTACTGAAGTGCCCTTGTGTACATTTGTTTTGTAATTTACCAAAGTACTACCTGAGTGTATAATGACTCCTGCAGTGAGTTAATGTAATTGCTGCTTTGACCATTGTTTTAAATCTGTGTACTAGAGTAACTGTGAGCAGAATGAAATCACATTATCTCAGTGTTCAAAATATCATTCTAATAAAGTACATGCATTAAACAATTTTAAAAAAAACAAAAAAAAAAAAAAAAAA

[0143] TABLE 35 Protein Sequence of PN7740 (SEQ ID NO:4)MSTAALITLVRSGGNQVRRRVLLSSRLLQDDRRVTPTCHSSTSEPRCSRFDPDGSGSPATWDNFGTWDNRIDEPILLPPSTKYGKPIPKISLENVGCASQIGKRKENEDRFDFAQLTDEVLYFAVYDGHGGPAAADFCHTHMEKCIMDLLPKEKNLETLLTLAFLEIDKAFSSHARLSADATLLTSGTTATVALLRDGIELVVASVGDSRAILCRKGKPMKLTIDHTPERKDEKERIKKCGGFVAWNSLGQPHVNGRLAMTRSIGDLDLKTSGVIAEPETKRIKLHHADDSFLVLTTDGINFMVNSQEICDFVNQCHDPNEAAHAVTEQAIQYGTEDNSTAVVVPFGAWGKYKNSEINFSFSRSFASSGRWA

[0144] TABLE 36 Ex. Bait aa GenBank Sw-Pr Prey aa GenBank Sw-Pr 2 BAT3 271-480 M33519 P46379 glypican  400-483 X54232 P35052 3 BAT3  740-1040M33519 P46379 LRP2   1-304 U33837 P98164 4 BAT3  740-1040 M33519 P46379LRPAP1  11-361 M63959 P30533 5 BAT3  740-1040 M33519 P46379transthyretin   7-148 X59498 P02766 6 Fe65  360-552 L77864 PN7740 27-322 7 Mint 1  739-837 AF047347 Q02410 GS  49-212 X59834 P15104 8Mint 1  447-758 AF047347 Q02410 KIAA0427  364-589 AB007887 9 PS1   1-91L42110 Q15720 Mint 1  471-822 AF047347 Q02410 10 CASK  306-574 AF032119Q43215 dystrophin  909-1280 M18533 P11532 11 CIB   1-191 U82226 Q99828S1P  442-619 NM_003791 12 Mint 2   1-210 AF047348 Q99767 S1P  765-859NM_003791 13 PS1   1-91 L42110 Q15720 P-gLycerate DH   1-266 NM_006623O43175 14 PS1   1-91 L42110 Q15720 beta-ETF  31-242 X71129 P38117 15 PS1  1-91 L42110 Q15720 GAPDH   2-190 M17851 P04406 16 PS2   1-97 L44577P49810 GAPDH   2-190 M17851 P04406 17 CIB   1-137 U82226 Q99828 ATPsynthase  229-459 X03559 P06576 18 KIAA0443  901-1200 AB007903PI-4-kinase  567-854 L36151 P42356 19 KIAA0443  901-1200 AB0079035HT-2AR  27-132 X57830 P28223 20 KIAAO351  301-557 AB002349 TRIO 475-733 U42390 21 CIB   1-191 U82226 Q99828 MLK2  305-549 X90846 Q0277922 BAX  50-107 L22474 Q07812 slo K⁺ channel  643-993 U13913 23 FAK2 673-866 L49207 Q14289 SUR1  121-270 AF087138 Q09428 24 Mint 2   1-210AF047348 Q99767 PDE-9A  269-593 AF048837 O76083 25 CIB   1-191 U82226Q99828 SCD2  320-359 Y13647 O00767 26 rab11   1-137 X56740 P24410 FAK 726-1003 L13616 Q14291 27 FAK  724-1052 L13616 Q14291 casein kinase II 264-351 M55268 P19784 28 FAK  724-1052 L13616 Q14291 GST trans. M3 15-226 J05459 P21266 29 bcr 1206-1271 NM_004327 P11274 PSD95  110-266NM_001365 P78352 30 bcr 1206-1271 NM_004327 P11274 DLG3  94-506 U49089Q92796 31 bcr  856-1226 NM_004327 P11274 Semaphorin F  670-821 32 bcr1206-1271 NM_04327 P11274 HTF4A  296-494 M83233 Q99081 33 bcr 1134-1271NM_004327 P11274 SRCAP 1916-2088 AF143946

Example 34 Yeast Two-Hybrid System

[0145] The principles and methods of the yeast two-hybrid systems havebeen described in detail (Bartel and Fields, 1997). The following isthus a description of the particular procedure that was used for thefinding of the interaction between PSD95 and PN7740.

[0146] The cDNA encoding the bait protein was generated by PCR from cDNAprepared from a desired tissue. Gene-specific primers were synthesizedwith appropriate short tails added at their 5′ ends to provide homologyto the vector PGBT.Q. The tail for the forward primer was5′-CCGCCACCATGGAATTA-3′ (SEQ ID NO:5) and the tail for the reverseprimer was 5′-TGCGGCCGCTAGTCGA -3′ (SEQ ID NO:6). The tailed PCR productwas then subjected to a secondary PCR reaction that extended the lengthof the tails and therefore the homology to the vector to facilitatecloning by homologous recombination. The secondary PCR reaction involvesseveral steps, starting with the extension of the 3′ ends of each tailby direct priming on the vector. This extension creates homology tosecondary primers that correspond to vector sequences further upstreamand downstream, respectively, from the original short tails. Thesecondary forward primer was 5′-CGCAGGAAACAGCTATGA-3′ (SEQ ID NO:7) andthe secondary reverse primer was 5′-TTGTAAAACGACGGCCAG-3′ (SEQ ID NO:8).The secondary primers allow complementary strand synthesis of theextended tailed product. Once both 3′ ends of the bait fragment havebeen extended it is amplified with the secondary primers. The product isthen introduced by recombination into the yeast expression vectorpGBT.Q, which is a close derivative of pGBT.C (Bartel et al.1996) inwhich the polylinker site has been modified to include M13 sequencingsites. The new construct was selected directly in the yeast strainPNY200 for its ability to drive tryptophane synthesis (genotype of thisstrain: MAT αtrp1-901leu2-3,112ura3-52his3-200 ade2 gal4Δgal80). Inthese yeast cells, the bait was produced as a C-terminal fusion proteinwith the DNA binding domain of the transcription factor Gal4 (aminoacids 1 to 147). Prey libraries were transformed into the yeast strainBK100 (genotype of this strain: MATαtrp1-901leu2-3,112ura3-52his3-200gal4Δgal8 LYS2::GAL-HIS3GAL2-ADE2 met2::GAL7-lacZ), and selectedfor the ability to drive leucine synthesis. In these yeast cells, eachcDNA was expressed as a fusion protein with the transcription activationdomain of the transcription factor Gal4 (amino acids 768 to 881) and a 9amino acid hemagglutinin epitope tag. PNY200 cells (MATα mating type),expressing the bait, were then mated with BK100 cells (MATα matingtype), expressing prey proteins from a prey library. The resultingdiploid yeast cells expressing proteins interacting with the baitprotein were selected for the ability to synthesize tryptophan, leucine,histidine, and adenine. DNA was prepared from each clone, transformed byelectroporation into E. coli strain KC8 (Clontech KC8 electrocompetentcells, Catalog No. C2023-1), and the cells were selected onampicillin-containing plates in the absence of either tryptophane(selection for the bait plasmid) or leucine (selection for the libraryplasmid). DNA for both plasmids was prepared and sequenced by thedideoxynucleotide chain termination method. The identity of the baitcDNA insert was confirmed and the cDNA insert from the prey libraryplasmid was identified using the BLAST program to search against publicnucleotide and protein databases. Plasmids from the prey library werethen individually transformed into yeast cells together with a plasmiddriving the synthesis of lamin and 5 other test proteins, respectively,fused to the Gal4 DNA binding domain. Clones that gave a positive signalin the β-galactosidase assay were considered false-positives anddiscarded. Plasmids for the remaining clones were transformed into yeastcells together with the original bait plasmid. Clones that gave apositive signal in the β-galactosidase assay were considered truepositives.

[0147] In this example, amino acids 149-255 of PSD95 (GenBank (GB)accession No. NM_(—)001365) was used as bait. One clone that wasidentified by this procedure included amino acids 27-321 of novelprotein PN7740.

Example 35 Generation of Polyclonal Antibody against BAT3-GlypicanComplex

[0148] As shown above, BAT3 interacts with glypican to form a complex. Acomplex of the two proteins is prepared, e.g., by mixing purifiedpreparations of each of the two proteins. If desired, the proteincomplex can be stabilized by cross-linking the proteins in the complexby methods known to those of skill in the art. The protein complex isused to immunize rabbits and mice using a procedure similar to the onedescribed by Harlow et al. (1988). This procedure has been shown togenerate Abs against various other proteins (for example, see Kraemer etal., 1993).

[0149] Briefly, purified protein complex is used as an immunogen inrabbits. Rabbits are immunized with 100 μg of the protein in completeFreund's adjuvant and boosted twice in three-week intervals, first with100 μg of immunogen in incomplete Freund's adjuvant, and followed by 100μg of immunogen in PBS. Antibody-containing serum is collected two weeksthereafter. The antisera is preadsorbed with BAT3 and glypican, suchthat the remaining antisera comprises antibodies which bindconformational epitopes, i.e., complex-specific epitopes, present on theBAT3-glypican complex but not on the monomers.

[0150] Polyclonal antibodies against each of the complexes set forth inTables 1-33 are prepared in a similar manner by mixing the specifiedproteins together, immunizing an animal and isolating antibodiesspecific for the protein complex, but not for the individual proteins.

[0151] Polyclonal antibodies against the novel protein set forth inTable 35 is prepared in a similar manner by immunizing an animal withthe protein and isolating antibodies specific for the protein.

Example 36 Generation of Monoclonal Antibodies Specific forBAT3-Glypican Complex

[0152] Monoclonal antibodies are generated according to the followingprotocol. Mice are immunized with immunogen comprising BAT3-glypicancomplexes conjugated to keyhole limpet hemocyanin using glutaraldehydeor EDC as is well known in the art. The complexes can be prepared asdescribed in Example 35 may also be stabilized by crosslinking. Theimmunogen is mixed with an adjuvant. Each mouse receives four injectionsof 10 to 100 μg of immunogen, and after the fourth injection, bloodsamples are taken from the mice to determine if the serum containsantibodies to the immunogen. Serum titer is determined by ELISA or RIA.Mice with sera indicating the presence of antibody to the immunogen areselected for hybridoma production.

[0153] Spleens are removed from immune mice and a single-cell suspensionis prepared (Harlow et al., 1988). Cell fusions are performedessentially as described by Kohler and Milstein (1975). Briefly, P3.65.3myeloma cells (American Type Culture Collection, Rockville, Md.) or NS-1myeloma cells are fused with immune spleen cells using polyethyleneglycol as described by Harlow et al. (1988). Cells are plated at adensity of 2×10⁵ cells/well in 96-well tissue culture plates. Individualwells are examined for growth, and the supernatants of wells with growthare tested for the presence of BAT3-glypican complex-specific antibodiesby ELISA or RIA using BAT3-glypican complex as target protein. Cells inpositive wells are expanded and subcloned to establish and confirmmonoclonality.

[0154] Clones with the desired specificities are expanded and grown asascites in mice or in a hollow fiber system to produce sufficientquantities of antibodies for characterization and assay development.Antibodies are tested for binding to BAT3 alone or to glypican alone, todetermine which are specific for the BAT3-glypican complex as opposed tothose that bind to the individual proteins.

[0155] Monoclonal antibodies against each of the complexes set forth inTables 1-33 are prepared in a similar manner by mixing the specifiedproteins together, immunizing an animal, fusing spleen cells withmyeloma cells and isolating clones which produce antibodies specific forthe protein complex, but not for the individual proteins.

[0156] Monoclonal antibodies against the novel protein set forth inTable 35 are prepared in a similar manner by immunizing an animal withthe protein, fusing spleen cells with myeloma cells and isolating cloneswhich produce antibodies specific for the protein.

Example 37 In vitro Identification of Modulators for BAT3-GlypicanInteraction

[0157] The invention is useful in screening for agents, which modulatethe interaction of BAT3 and glypican. The knowledge that BAT3 andglypican form a complex is useful in designing such assays. Candidateagents are screened by mixing BAT3 and glypican (a) in the presence of acandidate agent and (b) in the absence of the candidate agent. Theamount of complex formed is measured for each sample. An agent modulatesthe interaction of BAT3 and glypican if the amount of complex formed inthe presence of the agent is greater than (promoting the interaction),or less than (inhibiting the interaction) the amount of complex formedin the absence of the agent. The amount of complex is measured by abinding assay that shows the formation of the complex, or by usingantibodies immunoreactive to the complex.

[0158] Briefly, a binding assay is performed in which immobilized BAT3is used to bind labeled glypican. The labeled glypican is contacted withthe immobilized BAT3 under aqueous conditions that permit specificbinding of the two proteins to form an BAT3-glypican complex in theabsence of an added test agent. Particular aqueous conditions may beselected according to conventional methods. Any reaction condition canbe used, as long as specific binding of BAT3-glypican occurs in thecontrol reaction. A parallel binding assay is performed in which thetest agent is added to the reaction mixture. The amount of labeledglypican bound to the immobilized BAT3 is determined for the reactionsin the absence or presence of the test agent. If the amount of bound,labeled glypican in the presence of the test agent is different than theamount of bound labeled glypican in the absence of the test agent, thetest agent is a modulator of the interaction of BAT3 and glypican.

[0159] Candidate agents for modulating the interaction of each of theprotein complexes set forth in Tables 1-33 are screened in vitro in asimilar manner.

Example 38 In vivo Identification of Modulators for BAT3-GlypicanInteraction

[0160] In addition to the in vitro method described in Example 37, an invivo assay can also be used to screen for agents that modulate theinteraction of BAT3 and glypican. Briefly, a yeast two-hybrid system isused in which the yeast cells express (1) a first fusion proteincomprising BAT3 or a fragment thereof and a first transcriptionalregulatory protein sequence, e.g., GAL4 activation domain, (2) a secondfusion protein comprising glypican or a fragment thereof and a secondtranscriptional regulatory protein sequence, e.g., GAL4 DNA-bindingdomain, and (3) a reporter gene, e.g., β-galactosidase, which istranscribed when an intermolecular complex comprising the first fusionprotein and the second fusion protein is formed. Parallel reactions areperformed in the absence of a test agent as the control and in thepresence of the test agent. A functional BAT3-glypican complex isdetected by detecting the amount of reporter gene expressed. If theamount of reporter gene expression in the presence of the test agent isdifferent than the amount of reporter gene expression in the absence ofthe test agent, the test agent is a modulator of the interaction of BAT3and glypican.

[0161] Candidate agents for modulating the interaction of each of theprotein complexes set forth in Tables 1-33 are screened in vivo in asimilar manner.

[0162] While the invention has been disclosed in this patent applicationby reference to the details of preferred embodiments of the invention,it is to be understood that the disclosure is intended in anillustrative rather than in a limiting sense, as it is contemplated thatmodifications will readily occur to those skilled in the art, within thespirit of the invention and the scope of the appended claims.

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1 8 1 40 DNA Artificial Sequence Description of Artificial Sequencetailfor forward primer for yeast two-hybrid system 1 gcaggaaaca gctatgaccatacagtcagc ggccgccacc 40 2 39 DNA Artificial Sequence Description ofArtificial Sequencetail for reverse primer for yeast two-hybrid system 2acggccagtc gcgtggagtg ttatgtcatg cggccgcta 39 3 2740 DNA Homo sapiensCDS (217)..(1332) 3 cgagaatttc cagcaggcaa ggcagtggcc gctttgactgcttgcttcgg agatccgaga 60 cgacggagaa ggcactctta tttaccgacc aagaaagctcctcccccgtc ctccgttagc 120 taattaaaac atttttcagg gacgtagcca tccagagacattccattatt gttccattga 180 cctttccctc atcactgagt cctttggagc tgagtt atgtca aca gct gcc tta 234 Met Ser Thr Ala Ala Leu 1 5 att act ttg gtc agaagt ggt ggg aac cag gtg aga agg aga gtg ctg 282 Ile Thr Leu Val Arg SerGly Gly Asn Gln Val Arg Arg Arg Val Leu 10 15 20 cta agc tcc cgc ctg ctgcag gac gac agg cgg gtg aca ccc acg tgc 330 Leu Ser Ser Arg Leu Leu GlnAsp Asp Arg Arg Val Thr Pro Thr Cys 25 30 35 cac agc tcc act tca gag cctagg tgt tct cgg ttt gac cca gat ggt 378 His Ser Ser Thr Ser Glu Pro ArgCys Ser Arg Phe Asp Pro Asp Gly 40 45 50 agt ggg agt cca gct acc tgg gacaat ttt ggg atc tgg gat aac cgc 426 Ser Gly Ser Pro Ala Thr Trp Asp AsnPhe Gly Ile Trp Asp Asn Arg 55 60 65 70 att gat gag cca att ctg ctg ccaccc agc att aag tat ggc aag cca 474 Ile Asp Glu Pro Ile Leu Leu Pro ProSer Ile Lys Tyr Gly Lys Pro 75 80 85 att ccc aaa atc agc ttg gaa aat gtgggg tgc gcc tca cag att ggc 522 Ile Pro Lys Ile Ser Leu Glu Asn Val GlyCys Ala Ser Gln Ile Gly 90 95 100 aaa cgg aaa gag aat gaa gat cgg tttgac ttc gct cag ctg aca gat 570 Lys Arg Lys Glu Asn Glu Asp Arg Phe AspPhe Ala Gln Leu Thr Asp 105 110 115 gag gtc ctg tac ttt gca gtg tat gatgga cac ggt gga cct gca gca 618 Glu Val Leu Tyr Phe Ala Val Tyr Asp GlyHis Gly Gly Pro Ala Ala 120 125 130 gct gat ttc tgt cat acc cac atg gagaaa tgt att atg gat ttg ctt 666 Ala Asp Phe Cys His Thr His Met Glu LysCys Ile Met Asp Leu Leu 135 140 145 150 cct aag gag aag aac ttg gaa actctg ttg acc ttg gct ttt cta gaa 714 Pro Lys Glu Lys Asn Leu Glu Thr LeuLeu Thr Leu Ala Phe Leu Glu 155 160 165 ata gat aaa gcc ttt tcg agt catgcc cgc ctg tct gct gat gca act 762 Ile Asp Lys Ala Phe Ser Ser His AlaArg Leu Ser Ala Asp Ala Thr 170 175 180 ctt ctg acc tct ggg act act gcaaca gta gcc cta ttg cga gat ggt 810 Leu Leu Thr Ser Gly Thr Thr Ala ThrVal Ala Leu Leu Arg Asp Gly 185 190 195 att gaa ctg gtt gta gcc agt gttggg gac agc cgg gct att ttg tgt 858 Ile Glu Leu Val Val Ala Ser Val GlyAsp Ser Arg Ala Ile Leu Cys 200 205 210 aga aaa gga aaa ccc atg aag ctgacc att gac cat act cca gaa aga 906 Arg Lys Gly Lys Pro Met Lys Leu ThrIle Asp His Thr Pro Glu Arg 215 220 225 230 aaa gat gaa aaa gaa agg atcaag aaa tgt ggt ggt ttt gta gct tgg 954 Lys Asp Glu Lys Glu Arg Ile LysLys Cys Gly Gly Phe Val Ala Trp 235 240 245 aat agt ttg ggg cag cct cacgta aat ggc agg ctt gca atg aca aga 1002 Asn Ser Leu Gly Gln Pro His ValAsn Gly Arg Leu Ala Met Thr Arg 250 255 260 agt att gga gat ttg gac cttaag acc agt ggt gtc ata gca gaa cct 1050 Ser Ile Gly Asp Leu Asp Leu LysThr Ser Gly Val Ile Ala Glu Pro 265 270 275 gaa act aag agg att aag ttacat cat gct gat gac agc ttc ctg gtc 1098 Glu Thr Lys Arg Ile Lys Leu HisHis Ala Asp Asp Ser Phe Leu Val 280 285 290 ctc acc aca gat gga att aacttc atg gtg aat agt caa gag att tgt 1146 Leu Thr Thr Asp Gly Ile Asn PheMet Val Asn Ser Gln Glu Ile Cys 295 300 305 310 gac ttt gtc aat cag tgccat gat ccc aac gaa gca gcc cat gcg gtg 1194 Asp Phe Val Asn Gln Cys HisAsp Pro Asn Glu Ala Ala His Ala Val 315 320 325 act gaa cag gca ata cagtac ggt act gag gat aac agt act gca gta 1242 Thr Glu Gln Ala Ile Gln TyrGly Thr Glu Asp Asn Ser Thr Ala Val 330 335 340 gta gtg cct ttt ggt gcctgg gga aaa tat aag aac tct gaa atc aac 1290 Val Val Pro Phe Gly Ala TrpGly Lys Tyr Lys Asn Ser Glu Ile Asn 345 350 355 ttc tca ttc agc aga agcttt gcc tcc agt gga cga tgg gcc 1332 Phe Ser Phe Ser Arg Ser Phe Ala SerSer Gly Arg Trp Ala 360 365 370 tgattaccag ctgggactta gagtttctgtgcaacagttt ttcactgagc atgtcaagaa 1392 actgataaga tcaaaaaggt ctcctaactcactagatcag cgcacaagtc agtgtaaacc 1452 acttagatag tagttttttc ataaatgctcatcatattta tgttccgctg tacatgttca 1512 gtataaatat atgtgtagtg aagctactgtgagtctttaa atggaaagag caaatgagaa 1572 gtggtttgga tacacttgat gagagatgagagtgtcacat taataatttt taagactctt 1632 aggcagctat gggtttcttt tgatcatttttgttctttat tcatttgaac acgtttttga 1692 agttcttcaa aactagtcag tttgaattttgacagctatt caatatgtga tctccaagtt 1752 taaaaaaatt tttttccaga cttccctaatcctaaaatgc gagtttttat ttttaataac 1812 tgtaccaagg aataagtatg aaaacagttctctgttacca tattttgtat tctggaccac 1872 ttactggtga aagcaaccat gcaaaagaaattaatttggc caggcacagt ggctcatgcc 1932 tgtaatccca aattgctggg attacagcactgtgccctcc taggaaatta ttttttaagt 1992 gaaattttat ttttattttt tttaggattttggtagagaa tgagtaggcc tactcatcaa 2052 tatcaaacag gacatttagt ttctttccttagaacagaca taaatttaat ttcatggtaa 2112 tatgataata agaaaatgct tctatttttctttagcacct ccatggttct catataccca 2172 tgtctgtaaa aagtgacatg agaattttgttgggttacat tttattgtat ttattagatt 2232 cgcttatata gatgacttag gcagaaataaagtcatgtct ttagaaggtg aacaagccaa 2292 cttgtgatgg cctgcctttt gcttttggcagttgggatga gaacaattga ctctcccatt 2352 ggttgttaga tagttgaaat ggtgcgttggtggtcatact tagtgttcta ggctgtgaaa 2412 tcatggagtt cttccacttc caagaatgactcatttgctg ttggattcta gtacagaatt 2472 tagcagcctg atgtgtcccc aaactgatttaatttctact gaagtgccct tgtgtacatt 2532 tgttttgtaa tttaccaaag tactacctgagtgtataatg actcctgcag tgagttaatg 2592 taattgctgc tttgaccatt gttttaaatctgtgtactag agtaactgtg agcagaatga 2652 aatcacatta tctcagtgtt caaaatatcattctaataaa gtacatgcat taaacaattt 2712 taaaaaaaac aaaaaaaaaa aaaaaaaa2740 4 372 PRT Homo sapiens 4 Met Ser Thr Ala Ala Leu Ile Thr Leu ValArg Ser Gly Gly Asn Gln 1 5 10 15 Val Arg Arg Arg Val Leu Leu Ser SerArg Leu Leu Gln Asp Asp Arg 20 25 30 Arg Val Thr Pro Thr Cys His Ser SerThr Ser Glu Pro Arg Cys Ser 35 40 45 Arg Phe Asp Pro Asp Gly Ser Gly SerPro Ala Thr Trp Asp Asn Phe 50 55 60 Gly Ile Trp Asp Asn Arg Ile Asp GluPro Ile Leu Leu Pro Pro Ser 65 70 75 80 Ile Lys Tyr Gly Lys Pro Ile ProLys Ile Ser Leu Glu Asn Val Gly 85 90 95 Cys Ala Ser Gln Ile Gly Lys ArgLys Glu Asn Glu Asp Arg Phe Asp 100 105 110 Phe Ala Gln Leu Thr Asp GluVal Leu Tyr Phe Ala Val Tyr Asp Gly 115 120 125 His Gly Gly Pro Ala AlaAla Asp Phe Cys His Thr His Met Glu Lys 130 135 140 Cys Ile Met Asp LeuLeu Pro Lys Glu Lys Asn Leu Glu Thr Leu Leu 145 150 155 160 Thr Leu AlaPhe Leu Glu Ile Asp Lys Ala Phe Ser Ser His Ala Arg 165 170 175 Leu SerAla Asp Ala Thr Leu Leu Thr Ser Gly Thr Thr Ala Thr Val 180 185 190 AlaLeu Leu Arg Asp Gly Ile Glu Leu Val Val Ala Ser Val Gly Asp 195 200 205Ser Arg Ala Ile Leu Cys Arg Lys Gly Lys Pro Met Lys Leu Thr Ile 210 215220 Asp His Thr Pro Glu Arg Lys Asp Glu Lys Glu Arg Ile Lys Lys Cys 225230 235 240 Gly Gly Phe Val Ala Trp Asn Ser Leu Gly Gln Pro His Val AsnGly 245 250 255 Arg Leu Ala Met Thr Arg Ser Ile Gly Asp Leu Asp Leu LysThr Ser 260 265 270 Gly Val Ile Ala Glu Pro Glu Thr Lys Arg Ile Lys LeuHis His Ala 275 280 285 Asp Asp Ser Phe Leu Val Leu Thr Thr Asp Gly IleAsn Phe Met Val 290 295 300 Asn Ser Gln Glu Ile Cys Asp Phe Val Asn GlnCys His Asp Pro Asn 305 310 315 320 Glu Ala Ala His Ala Val Thr Glu GlnAla Ile Gln Tyr Gly Thr Glu 325 330 335 Asp Asn Ser Thr Ala Val Val ValPro Phe Gly Ala Trp Gly Lys Tyr 340 345 350 Lys Asn Ser Glu Ile Asn PheSer Phe Ser Arg Ser Phe Ala Ser Ser 355 360 365 Gly Arg Trp Ala 370 5 17DNA Artificial Sequence Description of Artificial Sequencetail forforward primer for yeast two-hybrid system 5 ccgccaccat ggaatta 17 6 16DNA Artificial Sequence Description of Artificial Sequencetail forreverse primer for yeast two-hybrid system 6 tgcggccgct agtcga 16 7 18DNA Artificial Sequence Description of Artificial Sequencesecondaryforward primer for yeast two-hybrid system 7 cgcaggaaac agctatga 18 8 18DNA Artificial Sequence Description of Artificial Sequencesecondaryreverse primer for yeast two-hybrid system 8 ttctaaaacg acggccag 18

What is claimed is:
 1. An isolated protein complex comprising twoproteins, the protein complex selected from the group consisting of: (a)a complex of Fe65 and PN7740; (b) a complex of a fragment of Fe65 andPN7740; (c) a complex Fe65 and a fragment of PN7740; (d) a complex of afragment of Fe65 and a fragment of PN7740; (e) a complex of PSD95 andPN7740; (f) a complex of a fragment of PSD95 and PN7740; (g) a complexPSD95 and a fragment of PN7740; and (h) a complex of a fragment of PSD95and a fragment of PN7740;
 2. The protein complex of claim 1, whereinsaid protein complex comprises Fe65 and PN7740.
 3. The protein complexof claim 1, wherein said protein complex comprises PSD95 and PN7740. 4.The protein complex of claim 1, wherein said protein complex comprises afragment of Fe65 and PN7740 or Fe65 and a fragment of PN7740.
 5. Theprotein complex of claim 1, wherein said protein complex comprises afragment of PSD95 and PN7740 or PSD95 and a fragment of PN7740.
 6. Theprotein complex of claim 1, wherein said protein complex comprisesfragments of Fe65 and PN7740.
 7. The protein complex of claim 1, whereinsaid protein complex comprises fragments of PSD95 and PN7740.
 8. Anisolated antibody selectively immunoreactive with a protein complex ofclaim
 1. 9. The antibody of claim 5, wherein said antibody is amonoclonal antibody.
 10. A method for diagnosing a neurodegenerativedisorder in an animal, which comprises assaying for: (a) whether aprotein complex set forth in claim 1 is present in a tissue extract; (b)the ability of proteins to form a protein complex set forth in claim 1;and (c) a mutation in a gene encoding a protein of a protein complex setforth in claim
 1. 11. The method of claim 10, wherein said animal is ahuman.
 12. The method of claim 11, wherein said neurodegenerativedisorder is selected from the group consisting of Huntington's Disease,Parkinson's Disease, dimentia and Alzheimer's Disease.
 13. The method ofclaim 12, wherein said neurodegenerative disorder is Alzheimer'sDisease.
 14. The method of claim 10, wherein the diagnosis is for apredisposition to said neurodegenerative disorder.
 15. The method ofclaim 14, wherein said neurodegenerative disorder is selected from thegroup consisting of Huntington's Disease, Parkinson's Disease, dementiaand Alzheimer's Disease.
 16. The method of claim 15, wherein saidneurodegenerative disorder is Alzheimer's Disease.
 17. The method ofclaim 10, wherein the diagnosis is for the existence of saidneurodegenerative disorder.
 18. The method of claim 17, wherein saidneurodegenerative disorder is selected from the group consisting ofHuntington's Disease, Parkinson's Disease, dementia and Alzheimer'sDisease.
 19. The method of claim 18, wherein said neurodegenerativedisorder is Alzheimer's Disease.
 20. The method of claim 10, whereinsaid assay comprises a yeast two-hybrid assay.
 21. The method of claim10, wherein said assay comprises measuring in vitro a complex formed bycombining the proteins of the protein complex, said proteins isolatedfrom said animal.
 22. The method of claim 16, wherein said complex ismeasured by binding with an antibody specific for said complex.
 23. Themethod of claim 10, wherein said assay comprises mixing an antibodyspecific for said protein complex with a tissue extract from said animaland measuring the binding of said antibody.
 24. A method for determiningwhether a mutation in a gene encoding one of the proteins of a proteincomplex set forth in claim 1 is useful for diagnosing aneurodegenerative disorder, which comprises assaying for the ability ofsaid protein with said mutation to form a complex with the other proteinof said protein complex, wherein an inability to form said complex isindicative of said mutation being useful for diagnosing aneurodegenerative disorder.
 25. The method of claim 24, wherein saidgene is an animal gene.
 26. The method of claim 25, wherein said animalis a human.
 27. The method of claim 26, wherein said neurodegenerativedisorder is selected from the group consisting of Huntington's Disease,Parkinson's Disease, dementia and Alzheimer's Disease.
 28. The method ofclaim 27, wherein said neurodegenerative disorder is Alzheimer'sDisease.
 29. The method of claim 24, wherein the diagnosis is for apredisposition to a neurodegenerative disorder.
 30. The method of claim24, wherein the diagnosis is for the existence of a neurodegenerativedisorder.
 31. The method of claim 24, wherein said assay comprises ayeast two-hybrid assay.
 32. The method of claim 24, wherein said assaycomprises measuring in vitro a complex formed by combining the proteinsof the protein complex, said proteins isolated from an animal.
 33. Themethod of claim 32, wherein said animal is a human.
 34. The method ofclaim 32, wherein said complex is measured by binding with an antibodyspecific for said complex.
 35. A non-human animal model for aneurodegenerative disorder wherein the genome of said animal or anancestor thereof has been modified such that the formation of a proteincomplex set forth in claim 1 has been altered.
 36. The non-human animalmodel of claim 35, wherein said neurodegenerative disorder is selectedfrom the group consisting of Huntington's Disease, Parkinson's Disease,dimentia and Alzheimer's Disease.
 37. The non-human animal model ofclaim 36, wherein said neurodegenerative disorder is Alzheimer'sDisease.
 38. The non-human animal model of claim 35, wherein theformation of said protein complex has been altered as a result of: (a)over-expression of at least one of the proteins of said protein complex;(b) replacement of a gene for at least one of the proteins of saidprotein complex with a gene from a second animal and expression of saidprotein; (c) expression of a mutant form of at least one of the proteinsof said protein complex; (d) a lack of expression of at least one of theproteins of said protein complex; or (e) reduced expression of at leastone of the proteins of said protein complex.
 39. A cell line obtainedfrom the animal model of claim
 35. 40. A non-human animal model for aneurodegenerative disorder, wherein the biological activity of a proteincomplex set forth in claim 1 has been altered.
 41. The non-human animalmodel of claim 40, wherein said neurodegenerative disorder is selectedfrom the group consisting of Huntington's Disease, Parkinson's Disease,dimentia and Alzheimer's Disease.
 42. The non-human animal model ofclaim 41, wherein said neurodegenerative disorder is Alzheimer'sDisease.
 43. The non-human animal model of claim 40, wherein saidbiological activity has been altered as a result of: (a) disrupting theformation of said complex; or (b) disrupting the action of said complex.44. The non-human animal model of claim 43, wherein the formation ofsaid complex is disrupted by binding an antibody to at least one of theproteins which form said protein complex.
 45. The non-human animal modelof claim 43, wherein the action of said complex is disrupted by bindingan antibody to said complex.
 46. The non-human animal model of claim 43,wherein the formation of said complex is disrupted by binding a smallmolecule to at least one of the proteins which form said proteincomplex.
 47. The non-human animal model of claim 43, wherein the actionof said complex is disrupted by binding a small molecule to saidcomplex.
 48. A cell in which the genome of cells of said cell line hasbeen modified to produce at least one protein complex set forth inclaim
 1. 49. A cell line in which the genome of the cells of said cellline has been modified to eliminate at least one protein of a proteincomplex set forth in claim
 1. 50. A composition comprising: a firstexpression vector having a nucleic acid encoding a ligand or a homologueor derivative or fragment thereof, said ligand selected from the groupconsisting of Fe65 and PSD95; and a second expression vector having anucleic acid encoding PN7740, or a homologue or derivative or fragmentthereof.
 51. The composition of claim 50, wherein said ligand is Fe64.52. The composition of claim 50, wherein said ligand is PSD95.
 53. Ahost cell comprising: a first expression vector having a nucleic acidencoding a first protein which is ligand or a homologue or derivative orfragment thereof, wherein said ligand is selected from the groupconsisting of Fe65 and PSD95; and a second expression vector having anucleic acid encoding a second protein which is PN7740, or a homologueor derivative or fragment thereof.
 54. The host cell of claim 53,wherein said ligand is Fe65.
 55. The host cell of claim 53, wherein saidligand is PSD95.
 56. The host cell of claim 53, wherein said host cellis a yeast cell.
 57. The host cell of claim 53, wherein said first andsecond proteins are expressed in fusion proteins.
 58. The host cell ofclaim 53, wherein one of said first and second nucleic acids is linkedto a nucleic acid encoding a DNA binding domain, and the other of saidfirst and second nucleic acids is linked to a nucleic acid encoding atranscription-activation domain, whereby two fusion proteins can beproduced in said host cell.
 59. The host cell of claim 53, furthercomprising a reporter gene, wherein the expression of the reporter geneis determined by the interaction between the first protein and thesecond protein.
 60. An isolated protein complex having a first proteinwhich is Fe65 or a homologue or derivative or fragment thereofinteracting with a second protein which is PN7740 or a homologue orderivative or fragment thereof.
 61. The isolated protein complex ofclaim 60 wherein said first protein is Fe65 and said second protein isPN7740.
 62. The isolated protein complex of claim 60, wherein said firstprotein is a first fusion protein containing Fe65 or Fe65 homologue,derivative or fragment, and wherein said second protein is a secondfusion protein containing PN7740 or PN7740 homologue, derivative orfragment.
 63. A method for making the protein complex of claim 60,comprising the steps of: providing said first protein and said secondprotein; and contacting said first protein with said second protein. 64.A protein microarray comprising the protein complex according to claim60.
 65. A fusion protein having a first polypeptide covalently linked toa second polypeptide, wherein said first polypeptide is Fe65 or ahomologue or derivative or fragment thereof, and wherein said secondpolypeptide is PN7740 or a homologue or derivative or fragment thereof.66. A nucleic acid encoding the fusion protein of claim
 65. 67. Anisolated protein complex having a first protein which is PSD95 or ahomologue or derivative or fragment thereof interacting with a secondprotein which is PN7740 or a homologue or derivative or fragmentthereof.
 68. The isolated protein complex of claim 67 wherein said firstprotein is PSD95 and said second protein is PN7740.
 69. The isolatedprotein complex of claim 67, wherein said first protein is a firstfusion protein containing PSD95 or PSD95 homologue, derivative orfragment, and wherein said second protein is a second fusion proteincontaining PN7740 or PN7740 homologue, derivative or fragment.
 70. Amethod for making the protein complex of claim 67, comprising the stepsof: providing said first protein and said second protein; and contactingsaid first protein with said second protein.
 71. A protein microarraycomprising the protein complex according to claim
 67. 72. A fusionprotein having a first polypeptide covalently linked to a secondpolypeptide, wherein said first polypeptide is PSD95 or a homologue orderivative or fragment thereof, and wherein said second polypeptide isPN7740 or a homologue or derivative or fragment thereof.
 73. A nucleicacid encoding the fusion protein of claim 72.